Mercurial > repos > ktnyt > gembassy

comparison GEMBASSY-1.0.3/src/gcircularmap.c @ 0:8300eb051bea draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial upload
author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:8300eb051bea
1 /******************************************************************************
2 ** @source gcircularmap
3 **
4 ** Draws circular map of the genome
5 **
6 ** @author Copyright (C) 2012 Hidetoshi Itaya
7 ** @version 1.0.3
8 ** @modified 2012/1/20 Hidetoshi Itaya Created!
9 ** @modified 2013/6/16 Revision 1
10 ** @modified 2015/2/7 Refactor
11 ** @@
12 **
13 ** This program is free software; you can redistribute it and/or
14 ** modify it under the terms of the GNU General Public License
15 ** as published by the Free Software Foundation; either version 2
16 ** of the License, or (at your option) any later version.
17 **
18 ** This program is distributed in the hope that it will be useful,
19 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
20 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 ** GNU General Public License for more details.
22 **
23 ** You should have received a copy of the GNU General Public License
24 ** along with this program; if not, write to the Free Software
25 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
26 ******************************************************************************/
27
28 #include "emboss.h"
29 #include "soapH.h"
30 #include "GLANGSoapBinding.nsmap"
31 #include "soapClient.c"
32 #include "soapC.c"
33 #include "../gsoap/stdsoap2.c"
34 #include "glibs.h"
35
36
37
38
39 /* @prog gcircularmap ********************************************************
40 **
41 ** Draws circular map of the genome
42 **
43 ******************************************************************************/
44
45 int main(int argc, char *argv[])
46 {
47 embInitPV("gcircularmap", argc, argv, "GEMBASSY", "1.0.3");
48
49 struct soap soap;
50 struct ns1__circular_USCOREmapInputParams params;
51
52 AjPSeqall seqall;
53 AjPSeq seq;
54 AjPStr inseq = NULL;
55 AjPStr seqid = NULL;
56 AjBool accid = ajFalse;
57 AjPFile outf = NULL;
58 AjPStr filename = NULL;
59 AjPStr outfname = NULL;
60 AjPStr format = NULL;
61
62 ajint i;
63
64 char *in0;
65 char *result;
66
67 seqall = ajAcdGetSeqall("sequence");
68 filename = ajAcdGetString("goutfile");
69 accid = ajAcdGetBoolean("accid");
70 format = ajAcdGetString("format");
71
72 params.gmap = 0;
73
74 i = 0;
75
76 while(ajSeqallNext(seqall, &seq))
77 {
78 soap_init(&soap);
79
80 soap.send_timeout = 0;
81 soap.recv_timeout = 0;
82
83 inseq = NULL;
84
85 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
86
87 if(ajStrGetLen(seqid) == 0)
88 {
89 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
90 }
91
92 if(ajStrGetLen(seqid) == 0)
93 {
94 ajWarn("No valid header information\n");
95 }
96
97 if(accid || !gFormatGenbank(seq, &inseq))
98 {
99 if(!accid)
100 {
101 ajWarn("Sequence does not have features\n"
102 "Proceeding with sequence accession ID:%S\n", seqid);
103 }
104
105 if(!gValID(seqid))
106 {
107 ajDie("Invalid accession ID:%S, exiting\n", seqid);
108 }
109
110 ajStrAssignS(&inseq, seqid);
111 }
112
113 in0 = ajCharNewS(inseq);
114
115 if(soap_call_ns1__circular_USCOREmap(
116 &soap,
117 NULL,
118 NULL,
119 in0,
120 &params,
121 &result
122 ) == SOAP_OK)
123 {
124 ++i;
125
126 outfname = ajStrNewS(ajFmtStr("%S.%d.%S",
127 filename,
128 i,
129 format));
130
131 outf = ajFileNewOutNameS(outfname);
132
133 if(!outf)
134 {
135 ajDie("File open error\n");
136 }
137
138 if(!ajStrMatchC(format, "svg"))
139 {
140 if(!gHttpConvertC(result, &outf, ajStrNewC("svg"), format))
141 {
142 ajDie("File downloading error from:\n%s\n", result);
143 }
144 else
145 {
146 ajFmtPrint("Created %S\n", outfname);
147 }
148 }
149 else
150 {
151 if(!gHttpGetBinC(result, &outf))
152 {
153 ajDie("File downloading error from:\n%s\n", result);
154 }
155 else
156 {
157 ajFmtPrint("Created %S\n", outfname);
158 }
159 }
160
161 ajStrDel(&outfname);
162 }
163 else
164 {
165 soap_print_fault(&soap, stderr);
166 }
167
168 soap_destroy(&soap);
169 soap_end(&soap);
170 soap_done(&soap);
171
172 AJFREE(in0);
173
174 ajStrDel(&seqid);
175 ajStrDel(&inseq);
176 }
177
178 ajSeqallDel(&seqall);
179 ajSeqDel(&seq);
180
181 ajStrDel(&filename);
182
183 embExit();
184
185 return 0;
186 }