1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
|
/* @source ajobodb ************************************************************
**
** AJAX OBODB (OBO database) functions
**
** These functions control all aspects of AJAX obo database access
**
** @author Copyright (C) 2010 Peter Rice
** @version $Revision: 1.15 $
** @modified Sep 2010 pmr first version
** @modified $Date: 2012/04/26 17:36:15 $ by $Author: mks $
** @@
**
** This library is free software; you can redistribute it and/or
** modify it under the terms of the GNU Lesser General Public
** License as published by the Free Software Foundation; either
** version 2.1 of the License, or (at your option) any later version.
**
** This library is distributed in the hope that it will be useful,
** but WITHOUT ANY WARRANTY; without even the implied warranty of
** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
** Lesser General Public License for more details.
**
** You should have received a copy of the GNU Lesser General Public
** License along with this library; if not, write to the Free Software
** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
** MA 02110-1301, USA.
**
******************************************************************************/
#include "ajlib.h"
#include "ajobodb.h"
#include "ajoboread.h"
#include "ajcall.h"
#include <limits.h>
#include <stdarg.h>
#include <sys/types.h>
#ifndef WIN32
#include <sys/socket.h>
#include <netinet/in.h>
#include <arpa/inet.h>
#include <errno.h>
#include <signal.h>
#include <netdb.h>
#include <dirent.h>
#include <unistd.h>
#else
#include <winsock2.h>
#include <ws2tcpip.h>
#endif
/* @funclist oboAccess ********************************************************
**
** Functions to access each database or obo access method
**
******************************************************************************/
static AjOOboAccess oboAccess[] =
{
/* Name AccessFunction FreeFunction
Qlink, Description
Alias Entry Query All Chunk Padding */
{
NULL, NULL, NULL,
NULL, NULL,
AJFALSE, AJFALSE, AJFALSE, AJFALSE, AJFALSE, AJFALSE
},
{
NULL, NULL, NULL,
NULL, NULL,
AJFALSE, AJFALSE, AJFALSE, AJFALSE, AJFALSE, AJFALSE
}
};
/* @func ajObodbInit **********************************************************
**
** Initialise obo database internals
**
** @return [void]
**
** @release 6.4.0
******************************************************************************/
void ajObodbInit(void)
{
AjPTable table;
ajuint i = 0;
table = ajOboaccessGetDb();
while(oboAccess[i].Name)
{
ajCallTableRegister(table, oboAccess[i].Name, (void*) &oboAccess[i]);
i++;
}
return;
}
/* @func ajObodbPrintAccess ***************************************************
**
** Reports the internal data structures
**
** @param [u] outf [AjPFile] Output file
** @param [r] full [AjBool] Full report (usually ajFalse)
** @return [void]
**
** @release 6.4.0
** @@
******************************************************************************/
void ajObodbPrintAccess(AjPFile outf, AjBool full)
{
ajint i = 0;
ajFmtPrintF(outf, "\n");
ajFmtPrintF(outf, "# Obo term access methods\n");
ajFmtPrintF(outf, "# Name Alias Entry Query All Description\n");
ajFmtPrintF(outf, "\n");
ajFmtPrintF(outf, "method {\n");
for(i=0; oboAccess[i].Name; i++)
if(full || !oboAccess[i].Alias)
ajFmtPrintF(outf, " %-10s %5B %5B %5B %5B \"%s\"\n",
oboAccess[i].Name, oboAccess[i].Alias,
oboAccess[i].Entry, oboAccess[i].Query,
oboAccess[i].All, oboAccess[i].Desc);
ajFmtPrintF(outf, "}\n\n");
return;
}
/* @func ajObodbExit **********************************************************
**
** Cleans up obo database processing internal memory
**
** @return [void]
**
** @release 6.4.0
** @@
******************************************************************************/
void ajObodbExit(void)
{
return;
}
|
