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
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
|
/* @include ensgvgenotype *****************************************************
**
** Ensembl Genetic Variation Genotype functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.9 $
** @modified 2009 by Alan Bleasby for incorporation into EMBOSS core
** @modified $Date: 2013/02/17 13:07:17 $ 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.
**
******************************************************************************/
#ifndef ENSGVGENOTYPE_H
#define ENSGVGENOTYPE_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ensgvdata.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
AjBool ensUtilityCharSort(char *string);
char ensUtilityBaseAmbiguityFromString(const char *basestr);
const char* ensUtilityBaseAmbiguityToString(char ambiguitychar);
/* Ensembl Genetic Variation Genotype */
EnsPGvgenotype ensGvgenotypeNewCpy(const EnsPGvgenotype gvg);
EnsPGvgenotype ensGvgenotypeNewIni(EnsPGvgenotypeadaptor gvga,
ajuint identifier,
EnsPGvvariation gvv,
AjPList alleles,
AjPStr subhandle,
ajuint subidentifier);
EnsPGvgenotype ensGvgenotypeNewRef(EnsPGvgenotype gvg);
void ensGvgenotypeDel(EnsPGvgenotype *Pgvg);
EnsPGvgenotypeadaptor ensGvgenotypeGetAdaptor(const EnsPGvgenotype gvg);
const AjPList ensGvgenotypeGetAlleles(const EnsPGvgenotype gvg);
EnsPGvvariation ensGvgenotypeGetGvvariation(const EnsPGvgenotype gvg);
ajuint ensGvgenotypeGetIdentifier(const EnsPGvgenotype gvg);
AjPStr ensGvgenotypeGetSubhandle(const EnsPGvgenotype gvg);
ajuint ensGvgenotypeGetSubidentifier(const EnsPGvgenotype gvg);
AjBool ensGvgenotypeSetAdaptor(EnsPGvgenotype gvg,
EnsPGvgenotypeadaptor gvga);
AjBool ensGvgenotypeSetGvvariation(EnsPGvgenotype gvg,
EnsPGvvariation gvv);
AjBool ensGvgenotypeSetIdentifier(EnsPGvgenotype gvg,
ajuint identifier);
AjBool ensGvgenotypeSetSubhandle(EnsPGvgenotype gvg,
AjPStr subhandle);
AjBool ensGvgenotypeSetSubidentifier(EnsPGvgenotype gvg,
ajuint subidentifier);
AjBool ensGvgenotypeAddAllele(EnsPGvgenotype gvg,
AjPStr allele);
AjBool ensGvgenotypeAddAllelenumber(EnsPGvgenotype gvg,
ajuint number,
AjPStr allele);
AjBool ensGvgenotypeAddGvgenotypecode(EnsPGvgenotype gvg,
EnsPGvgenotypecode gvgc);
AjBool ensGvgenotypeTrace(const EnsPGvgenotype gvg, ajuint level);
const AjPStr ensGvgenotypeCalculateAllelenumber(const EnsPGvgenotype gvg,
ajuint number);
size_t ensGvgenotypeCalculateMemsize(const EnsPGvgenotype gvg);
AjBool ensGvgenotypeFetchAlleleNumber(const EnsPGvgenotype gvg,
ajuint number,
AjPStr *Pallele);
AjBool ensGvgenotypeFetchAlleleString(const EnsPGvgenotype gvg,
AjPStr *Pstring);
/* Ensembl Genetic Variation Genotype Adaptor */
EnsPGvgenotypeadaptor ensRegistryGetGvgenotypeadaptor(
EnsPDatabaseadaptor dba);
/* Ensembl Genetic Variation Genotype Code */
EnsPGvgenotypecode ensGvgenotypecodeNewCpy(const EnsPGvgenotypecode gvgc);
EnsPGvgenotypecode ensGvgenotypecodeNewIni(EnsPGvgenotypecodeadaptor gvgca,
ajuint identifier,
AjPList alleles);
EnsPGvgenotypecode ensGvgenotypecodeNewRef(EnsPGvgenotypecode gvgc);
void ensGvgenotypecodeDel(EnsPGvgenotypecode *Pgvgc);
EnsPGvgenotypecodeadaptor ensGvgenotypecodeGetAdaptor(
const EnsPGvgenotypecode gvgc);
const AjPList ensGvgenotypecodeGetAlleles(
const EnsPGvgenotypecode gvgc);
ajuint ensGvgenotypecodeGetIdentifier(
const EnsPGvgenotypecode gvgc);
AjBool ensGvgenotypecodeSetAdaptor(EnsPGvgenotypecode gvgc,
EnsPGvgenotypecodeadaptor gvgca);
AjBool ensGvgenotypecodeSetIdentifier(EnsPGvgenotypecode gvgc,
ajuint identifier);
AjBool ensGvgenotypecodeAddAllele(EnsPGvgenotypecode gvgc, AjPStr allele);
AjBool ensGvgenotypecodeTrace(const EnsPGvgenotypecode gvgc, ajuint level);
size_t ensGvgenotypecodeCalculateMemsize(const EnsPGvgenotypecode gvgc);
/* Ensembl Genetic Variation Genotype Code Adaptor */
EnsPGvgenotypecodeadaptor ensRegistryGetGvgenotypecodeadaptor(
EnsPDatabaseadaptor dba);
EnsPGvgenotypecodeadaptor ensGvgenotypecodeadaptorNew(
EnsPDatabaseadaptor dba);
void ensGvgenotypecodeadaptorDel(
EnsPGvgenotypecodeadaptor *Pgvgca);
EnsPBaseadaptor ensGvgenotypecodeadaptorGetBaseadaptor(
EnsPGvgenotypecodeadaptor gvgca);
EnsPDatabaseadaptor ensGvgenotypecodeadaptorGetDatabaseadaptor(
EnsPGvgenotypecodeadaptor gvgca);
EnsPGvbaseadaptor ensGvgenotypecodeadaptorGetGvbaseadaptor(
EnsPGvgenotypecodeadaptor gvgca);
AjBool ensGvgenotypecodeadaptorFetchAllbyIdentifiers(
EnsPGvgenotypecodeadaptor gvgca,
AjPTable gvgcs);
/*
** End of prototype definitions
*/
AJ_END_DECLS
#endif /* !ENSGVGENOTYPE_H */
|
