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1 /******************************************************************************
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2 ** @source ggenomemap3
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3 **
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4 ** Draws the map of the genome (Version 3)
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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 Refactor
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11 ** @@
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12 **
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13 ** This program is free software; you can redistribute it and/or
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14 ** modify it under the terms of the GNU General Public License
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15 ** as published by the Free Software Foundation; either version 2
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16 ** of the License, or (at your option) any later version.
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17 **
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18 ** This program is distributed in the hope that it will be useful,
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19 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
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20 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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21 ** GNU General Public License for more details.
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22 **
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23 ** You should have received a copy of the GNU General Public License
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24 ** along with this program; if not, write to the Free Software
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25 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
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26 ******************************************************************************/
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27
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28 #include "emboss.h"
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29 #include "soapH.h"
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30 #include "GLANGSoapBinding.nsmap"
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31 #include "soapClient.c"
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32 #include "soapC.c"
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33 #include "../gsoap/stdsoap2.c"
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34 #include "glibs.h"
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35
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36
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37
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38
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39 /* @prog ggenomemap3 **********************************************************
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40 **
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41 ** Draws the map of the genome (Version 3)
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42 **
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43 ******************************************************************************/
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44
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45 int main(int argc, char *argv[])
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46 {
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47 embInitPV("ggenomemap3", argc, argv, "GEMBASSY", "1.0.3");
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48
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49 struct soap soap;
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50 struct ns1__genome_USCOREmap3InputParams params;
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51
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52 AjPSeqall seqall;
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53 AjPSeq seq;
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54 AjPStr inseq = NULL;
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55 AjPStr seqid = NULL;
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56 ajint width;
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57 ajint height;
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58 AjBool accid = ajFalse;
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59 AjPFile outf = NULL;
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60 AjPStr filename = NULL;
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61 AjPStr outfname = NULL;
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62 AjPStr format = NULL;
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63
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64 ajint i;
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65
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66 char *in0;
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67 char *result;
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68
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69 seqall = ajAcdGetSeqall("sequence");
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70 width = ajAcdGetInt("width");
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71 height = ajAcdGetInt("height");
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72 filename = ajAcdGetString("goutfile");
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73 accid = ajAcdGetBoolean("accid");
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74 format = ajAcdGetString("format");
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75
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76 params.width = width;
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77 params.height = height;
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78 params.gmap = 0;
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79 params.datafilename = "";
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80 params.output = "g";
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81
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82 i = 0;
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83
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84 while(ajSeqallNext(seqall, &seq))
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85 {
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86
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87 soap_init(&soap);
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88
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89 soap.send_timeout = 0;
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90 soap.recv_timeout = 0;
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91
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92 inseq = NULL;
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93
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94 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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95
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96 if(!ajStrGetLen(seqid))
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97 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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98
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99 if(!ajStrGetLen(seqid))
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100 {
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101 ajWarn("No valid header information\n");
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102 }
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103
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104 if(accid || !gFormatGenbank(seq, &inseq))
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105 {
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106 if(!accid)
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107 ajWarn("Sequence does not have features\n"
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108 "Proceeding with sequence accession ID:%S\n", seqid);
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109
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110 if(!gValID(seqid))
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111 {
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112 ajDie("Invalid accession ID:%S, exiting\n", seqid);
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113 }
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114
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115 ajStrAssignS(&inseq, seqid);
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116 }
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117
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118 in0 = ajCharNewS(inseq);
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119
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120 if(soap_call_ns1__genome_USCOREmap3(
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121 &soap,
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122 NULL,
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123 NULL,
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124 in0,
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125 ¶ms,
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126 &result
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127 ) == SOAP_OK)
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128 {
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129 ++i;
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130
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131 outfname = ajStrNewS(ajFmtStr("%S.%d.%S",
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132 filename,
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133 i,
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134 format));
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135
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136 outf = ajFileNewOutNameS(outfname);
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137
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138 if(!outf)
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139 {
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140 ajDie("File open error\n");
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141 }
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142
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143 if(!ajStrMatchC(format, "png"))
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144 {
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145 if(!gHttpConvertC(result, &outf, ajStrNewC("png"), format))
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146 {
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147 ajDie("File downloading error from:\n%s\n", result);
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148 }
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149 else
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150 {
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151 ajFmtPrint("Created %S\n", outfname);
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152 }
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153 }
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154 else
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155 {
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156 if(!gHttpGetBinC(result, &outf))
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157 {
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158 ajDie("File downloading error from:\n%s\n", result);
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159 }
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160 else
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161 {
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162 ajFmtPrint("Created %S\n", outfname);
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163 }
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164 }
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165
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166 ajStrDel(&outfname);
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167 }
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168 else
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169 {
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170 soap_print_fault(&soap, stderr);
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171 }
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172
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173 soap_destroy(&soap);
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174 soap_end(&soap);
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175 soap_done(&soap);
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176
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177 AJFREE(in0);
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178
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179 ajStrDel(&seqid);
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180 ajStrDel(&inseq);
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181 }
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182
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183 ajSeqallDel(&seqall);
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184 ajSeqDel(&seq);
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185
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186 ajStrDel(&filename);
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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 }
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