1 /** @source edamhasoutput
2 **
3 ** Find EDAM ontology terms by has_output relationship
4 **
5 ** @author Copyright (C) 2010 Jon Ison / EMBOSS
6 ** @version 1 First version</replaceable>
7 ** @modified July 2010 Jon Ison First version</replaceable>
8 ** @@
9 **
10 ** This program is free software; you can redistribute it and/or
11 ** modify it under the terms of the GNU General Public License
12 ** as published by the Free Software Foundation; either version 2
13 ** of the License, or (at your option) any later version.
14 **
15 ** This program is distributed in the hope that it will be useful,
16 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
17 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18 ** GNU General Public License for more details.
19 **
20 ** You should have received a copy of the GNU General Public License
21 ** along with this program; if not, write to the Free Software
22 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23 ********************************************************************/
24
25
26 /* ==================================================================== */
27 /* ========================== include files =========================== */
28 /* ==================================================================== */
29
30 #include "emboss.h"
31
32 /* Inclusion of system and local header files goes here */
33
34
35
36 /* ==================================================================== */
37 /* ============================ constants ============================= */
38 /* ==================================================================== */
39
40 /* #define and enum statements go here */
41
42
43
44 /* ==================================================================== */
45 /* ======================== global variables ========================== */
46 /* ==================================================================== */
47
48 /* Global variables definitions go here */
49
50
51
52 /* ==================================================================== */
53 /* ============================== data ================================ */
54 /* ==================================================================== */
55
56 /* Definition of datatypes go here */
57
58
59
60 /* ==================================================================== */
61 /* ==================== function prototypes =========================== */
62 /* ==================================================================== */
63
64 /* Function prototypes for public (external) functions go here */
65
66
67
68
69 /* @prog edamhasoutput ********************************************************
70 **
71 ** Find EDAM ontology 'data' (identifier) terms by keyword
72 **
73 ******************************************************************************/
74
main(int argc,char ** argv)75 int main(int argc, char **argv)
76 {
77 /* Variable declarations */
78 AjPStr query;
79 AjPStr *namespace = NULL;
80 AjPOutfile outfile = NULL;
81 AjBool sensitive = ajFalse;
82 AjBool subclasses = ajFalse;
83 AjBool obsolete = ajTrue;
84
85 AjPObo obo = NULL;
86 AjPObo oborelate = NULL;
87 AjPObo obotest = NULL;
88 AjPOboin oboin = NULL;
89 AjPOboin oboinrelate = NULL;
90
91 AjPList obolist = ajListNew();
92
93 AjPStr oboqry = NULL;
94 AjPStr oboqryrelate = NULL;
95 AjPStr qrystr = NULL;
96 AjPTable obotable = NULL;
97 AjPTable nstable = NULL;
98 AjPTable foundtable = NULL;
99 const AjPStr name = NULL;
100
101 AjPStrTok handle = NULL;
102 ajuint i;
103 ajuint imax = 3;
104
105 const char* fields[] = {"id", "acc", "nam", "des"};
106
107 /* ACD processing */
108 embInit("edamhasoutput", argc, argv);
109
110 query = ajAcdGetString("identifier");
111 namespace = ajAcdGetList("namespace");
112 outfile = ajAcdGetOutobo("outfile");
113 sensitive = ajAcdGetBoolean("sensitive");
114 subclasses = ajAcdGetBoolean("subclasses");
115 obsolete = ajAcdGetBoolean("obsolete");
116
117 oboin = ajOboinNew();
118 obo = ajOboNew();
119 oboinrelate = ajOboinNew();
120 oborelate = ajOboNew();
121
122 foundtable = ajTablestrNew(600);
123 obotable = ajTablestrNew(600);
124 nstable = ajTablestrNew(6);
125
126 if(sensitive)
127 imax++;
128
129 for(i=0; namespace[i]; i++)
130 {
131 ajTablePut(nstable, namespace[i], (void*) 1);
132 }
133
134 handle = ajStrTokenNewC(query, ",");
135 while(ajStrTokenNextParse(handle, &qrystr))
136 {
137 for(i=0;i<imax;i++)
138 {
139 ajFmtPrintS(&oboqry, "edam-%s:%S", fields[i], qrystr);
140
141 ajOboinQryS(oboin, oboqry);
142
143 while(ajOboinRead(oboin, obo))
144 {
145 if(!obsolete && ajOboIsObsolete(obo))
146 continue;
147
148 ajListPushAppend(obolist, ajOboNewObo(obo));
149 if(subclasses)
150 ajOboGetTree(obo, obolist);
151
152 ajDebug("%S '%S' %Lu\n",
153 qrystr, obo->Id, ajListGetLength(obolist));
154 while(ajListGetLength(obolist))
155 {
156 ajListPop(obolist, (void**) &obotest);
157 if(!obsolete && ajOboIsObsolete(obotest))
158 {
159 ajOboDel(&obotest);
160 continue;
161 }
162
163 if(!ajTableMatchS(obotable, obotest->Id))
164 {
165 ajFmtPrintS(&oboqryrelate, "edam-hasout:%S",
166 obotest->Id);
167 ajOboinQryS(oboinrelate, oboqryrelate);
168 while(ajOboinRead(oboinrelate, oborelate))
169 {
170 if(!obsolete && ajOboIsObsolete(oborelate))
171 continue;
172
173 name = ajOboGetNamespace(oborelate);
174 if(ajTableMatchS(nstable, name))
175 {
176 if(!ajTableMatchS(foundtable, oborelate->Id))
177 {
178 ajObooutWrite(outfile, oborelate);
179 ajTablePut(foundtable,
180 ajStrNewS(oborelate->Id),
181 (void *) 1);
182 }
183 }
184 }
185 }
186 ajOboDel(&obotest);
187 }
188 }
189 }
190 }
191
192 /* Memory clean-up and exit */
193
194 ajListFree(&obolist);
195
196 ajStrTokenDel(&handle);
197 ajStrDel(&qrystr);
198 ajTablestrFreeKey(&obotable);
199 ajTablestrFreeKey(&foundtable);
200 ajTableFree(&nstable);
201
202 ajStrDel(&query);
203 for(i=0; namespace[i]; i++)
204 ajStrDel(&namespace[i]);
205 AJFREE(namespace);
206
207 ajStrDel(&oboqry);
208 ajStrDel(&oboqryrelate);
209 ajOboDel(&obo);
210 ajOboDel(&oborelate);
211 ajOboinDel(&oboin);
212 ajOboinDel(&oboinrelate);
213
214 ajOutfileClose(&outfile);
215
216 embExit();
217
218 return 0;
219 }
220
221
222 /* ==================================================================== */
223 /* ============================ functions ============================= */
224 /* ==================================================================== */
225
226