1 /** @source ontocount
2 **
3 ** Get number of ontology term(s) matching a query
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 ontocount ************************************************************
70 **
71 ** Count ontology term(s) matching a query
72 **
73 ******************************************************************************/
74
main(int argc,char ** argv)75 int main(int argc, char **argv)
76 {
77 /* Variable declarations */
78 AjPOboall oboall = NULL;
79 AjBool subclasses = ajFalse;
80 AjBool obsolete = ajFalse;
81 AjPFile outf = NULL;
82
83 AjPObo obo = NULL;
84 AjPObo obotest = NULL;
85
86 AjPList obolist = ajListNew();
87
88 AjPTable foundtable = NULL;
89 ajuint ifound = 0;
90 ajuint ikeep = 0;
91
92 /* ACD processing */
93 embInit("ontocount", argc, argv);
94
95 oboall = ajAcdGetOboall("oboterms");
96 outf = ajAcdGetOutfile("outfile");
97 subclasses = ajAcdGetBoolean("subclasses");
98 obsolete = ajAcdGetBoolean("obsolete");
99
100 foundtable = ajTablestrNew(600);
101
102 while(ajOboallNext(oboall, &obo))
103 {
104 ajListPushAppend(obolist, ajOboNewObo(obo));
105
106 if(subclasses)
107 ajOboGetTree(obo, obolist);
108
109 while(ajListGetLength(obolist))
110 {
111 ajListPop(obolist, (void**) &obotest);
112 if(!obsolete && ajOboIsObsolete(obotest))
113 {
114 ajOboDel(&obotest);
115 continue;
116 }
117
118 ifound++;
119 if(!ajTableMatchS(foundtable, obotest->Id))
120 {
121 ajTablePut(foundtable, ajStrNewS(obotest->Id),
122 (void *) 1);
123 ikeep++;
124 }
125 ajOboDel(&obotest);
126 }
127 }
128
129 ajFmtPrintF(outf, "%u\n", ikeep);
130
131 /* Memory clean-up and exit */
132
133 ajListFree(&obolist);
134
135 ajOboallDel(&oboall);
136 ajOboDel(&obo);
137 ajFileClose(&outf);
138 ajTablestrFreeKey(&foundtable);
139
140 embExit();
141
142 return 0;
143 }
144
145
146 /* ==================================================================== */
147 /* ============================ functions ============================= */
148 /* ==================================================================== */
149
150