annotate GEMBASSY-1.0.3/src/greporiter.c @ 0:8300eb051bea draft

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author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
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1 /******************************************************************************
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2 ** @source greporiter
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3 **
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4 ** Get the positions of replication origin and terminus
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5 **
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6 ** @author Copyright (C) 2012 Hidetoshi Itaya
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7 ** @version 1.0.3
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8 ** @modified 2012/1/20 Hidetoshi Itaya Created!
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9 ** @modified 2013/6/16 Revision 1
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10 ** @modified 2015/2/7 RESTify
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11 ** @modified 2015/2/7 Refactor
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12 ** @@
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13 **
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14 ** This program is free software; you can redistribute it and/or
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15 ** modify it under the terms of the GNU General Public License
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16 ** as published by the Free Software Foundation; either version 2
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17 ** of the License, or (at your option) any later version.
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18 **
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19 ** This program is distributed in the hope that it will be useful,
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20 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
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21 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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22 ** GNU General Public License for more details.
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23 **
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24 ** You should have received a copy of the GNU General Public License
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25 ** along with this program; if not, write to the Free Software
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26 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
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27 ******************************************************************************/
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28
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29 #include "emboss.h"
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30 #include "glibs.h"
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31
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32
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33
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34
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35 /* @prog greporiter *********************************************************
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36 **
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37 ** Get the positions of replication origin and terminus
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38 **
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39 ******************************************************************************/
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40
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41 int main(int argc, char *argv[])
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42 {
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43 embInitPV("greporiter", argc, argv, "GEMBASSY", "1.0.3");
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44
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45 AjPSeqall seqall;
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46 AjPSeq seq;
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47 AjPStr inseq = NULL;
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48
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49 AjBool accid = ajFalse;
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50 AjPStr restid = NULL;
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51 AjPStr seqid = NULL;
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52
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53 AjPStr base = NULL;
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54 AjPStr url = NULL;
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55
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56 AjBool oriloc = 0;
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57 AjBool gcskew = 0;
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58 AjBool dbonly = 0;
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59 ajint difthreshold = 0;
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60
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61 AjPFile outf = NULL;
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62
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63 AjPFile tmpfile = NULL;
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64 AjPStr tmpname = NULL;
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65 AjPStr fstname = NULL;
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66 AjPFilebuff tmp = NULL;
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67 AjPStr line = NULL;
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68 AjPSeqout tmpout = NULL;
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69
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70 AjPRegexp regex;
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71
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72 AjPStr ori = NULL;
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73 AjPStr ter = NULL;
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74
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75 seqall = ajAcdGetSeqall("sequence");
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76 difthreshold = ajAcdGetInt("difthreshold");
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77 oriloc = ajAcdGetBoolean("oriloc");
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78 gcskew = ajAcdGetBoolean("gcskew");
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79 dbonly = ajAcdGetBoolean("dbonly");
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80 accid = ajAcdGetBoolean("accid");
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81 outf = ajAcdGetOutfile("outfile");
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82
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83 base = ajStrNewC("rest.g-language.org");
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84
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85 gAssignUniqueName(&tmpname);
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86 gAssignUniqueName(&fstname);
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87 ajStrAppendC(&fstname, ".fasta");
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88
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89 while(ajSeqallNext(seqall, &seq))
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90 {
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91 inseq = ajStrNew();
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92
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93 tmpout = ajSeqoutNew();
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94
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95 if(!accid)
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96 {
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97 if(gFormatGenbank(seq, &inseq))
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98 {
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99 tmpfile = ajFileNewOutNameS(tmpname);
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100 if(!tmpfile)
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101 {
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102 ajDie("Output file (%S) open error\n", tmpname);
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103 }
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104 ajFmtPrintF(tmpfile, "%S", inseq);
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105 ajFileClose(&tmpfile);
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106 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
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107 gFilePostSS(url, tmpname, &restid);
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108 ajStrDel(&url);
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109 ajSysFileUnlinkS(tmpname);
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110 }
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111 else
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112 {
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113 if(!ajSeqoutOpenFilename(tmpout, fstname))
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114 {
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115 embExitBad();
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116 }
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117
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118 ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
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119 ajSeqoutWriteSeq(tmpout, seq);
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120 ajSeqoutClose(tmpout);
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121 ajSeqoutDel(&tmpout);
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122 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
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123 gFilePostSS(url, fstname, &restid);
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124 ajStrDel(&url);
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125 ajSysFileUnlinkS(fstname);
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126 }
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127 }
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128
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129 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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130
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131 if(ajStrGetLen(seqid) == 0)
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132 {
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133 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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134 }
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135
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136 if(ajStrGetLen(seqid) == 0)
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137 {
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138 ajWarn("No valid header information\n");
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139 }
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140
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141 if(accid)
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142 {
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143 ajStrAssignS(&restid, seqid);
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144 if(ajStrGetLen(seqid) == 0)
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145 {
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146 ajDie("Cannot proceed without header with -accid\n");
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147 }
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148
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149 if(!gValID(seqid))
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150 {
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151 ajDie("Invalid accession ID:%S, exiting\n", seqid);
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152 }
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153 }
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154
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155 url = ajStrNew();
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156
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157 ajFmtPrintS(&url, "http://%S/%S/rep_ori_ter/oriloc=%d/gcskew=%d/"
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158 "difthreshold=%d/dbonly=%d/", base, restid, oriloc, gcskew,
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159 difthreshold, dbonly);
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160
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161 if(!gFilebuffURLS(url, &tmp))
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162 {
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163 ajDie("Failed to download result from:\n%S\n", url);
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164 }
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165
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166 ajBuffreadLine(tmp, &line);
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167
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168 regex = ajRegCompC("([0-9]+),([0-9]+)");
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169
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170 if(ajRegExec(regex, line)) {
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171 if(ajRegSubI(regex, 1, &ori), ajRegSubI(regex, 2, &ter)) {
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172 ajFmtPrint("%S Origin: %S Terminus %S\n", seqid, ori, ter);
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173 }
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174 }
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175
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176 ajStrDel(&url);
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177 ajStrDel(&restid);
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178 ajStrDel(&seqid);
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179 ajStrDel(&inseq);
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180 }
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181
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182 ajFileClose(&outf);
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183
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184 ajSeqallDel(&seqall);
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185 ajSeqDel(&seq);
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186 ajStrDel(&base);
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187
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188 embExit();
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189
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190 return 0;
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191 }