/usr/lib/emboss/include/ensgvindividual.h is in emboss-lib 6.6.0+dfsg-3build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 | /* @include ensgvindividual ***************************************************
**
** Ensembl Genetic Variation Individual functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.16 $
** @modified 2009 by Alan Bleasby for incorporation into EMBOSS core
** @modified $Date: 2012/08/05 10:56:34 $ 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 ENSGVINDIVIDUAL_H
#define ENSGVINDIVIDUAL_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ensgvsample.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
/* Ensembl Genetic Variation Individual */
EnsPGvindividual ensGvindividualNewCpy(const EnsPGvindividual gvi);
EnsPGvindividual ensGvindividualNewIni(EnsPGvindividualadaptor gvia,
ajuint identifier,
EnsPGvsample gvs,
EnsPGvindividual father,
EnsPGvindividual mother,
EnsEGvindividualGender gender,
EnsEGvindividualType type,
AjPStr description);
EnsPGvindividual ensGvindividualNewRef(EnsPGvindividual gvi);
void ensGvindividualDel(EnsPGvindividual *Pgvi);
EnsPGvindividualadaptor ensGvindividualGetAdaptor(const EnsPGvindividual gvi);
AjPStr ensGvindividualGetDescription(const EnsPGvindividual gvi);
EnsPGvindividual ensGvindividualGetFather(const EnsPGvindividual gvi);
EnsEGvindividualGender ensGvindividualGetGender(const EnsPGvindividual gvi);
EnsPGvsample ensGvindividualGetGvsample(const EnsPGvindividual gvi);
ajuint ensGvindividualGetIdentifier(const EnsPGvindividual gvi);
EnsPGvindividual ensGvindividualGetMother(const EnsPGvindividual gvi);
EnsEGvindividualType ensGvindividualGetType(const EnsPGvindividual gvi);
AjBool ensGvindividualSetAdaptor(EnsPGvindividual gvi,
EnsPGvindividualadaptor gvia);
AjBool ensGvindividualSetDescription(EnsPGvindividual gvi,
AjPStr description);
AjBool ensGvindividualSetFather(EnsPGvindividual gvi,
EnsPGvindividual father);
AjBool ensGvindividualSetGender(EnsPGvindividual gvi,
EnsEGvindividualGender gender);
AjBool ensGvindividualSetGvsample(EnsPGvindividual gvi,
EnsPGvsample gvs);
AjBool ensGvindividualSetIdentifier(EnsPGvindividual gvi,
ajuint identifier);
AjBool ensGvindividualSetMother(EnsPGvindividual gvi,
EnsPGvindividual mother);
AjBool ensGvindividualSetType(EnsPGvindividual gvi,
EnsEGvindividualType type);
AjBool ensGvindividualTrace(const EnsPGvindividual gvi, ajuint level);
size_t ensGvindividualCalculateMemsize(const EnsPGvindividual gvi);
AjBool ensGvindividualFetchAllChildren(EnsPGvindividual gvi,
AjPList gvis);
AjBool ensGvindividualFetchAllGvpopulations(EnsPGvindividual gvi,
AjPList gvps);
EnsEGvindividualGender ensGvindividualGenderFromStr(const AjPStr gender);
const char *ensGvindividualGenderToChar(EnsEGvindividualGender gvig);
EnsEGvindividualType ensGvindividualTypeFromStr(const AjPStr type);
const char *ensGvindividualTypeToChar(EnsEGvindividualType gvit);
/* Ensembl Genetic Variation Individual Adaptor */
EnsPGvindividualadaptor ensRegistryGetGvindividualadaptor(
EnsPDatabaseadaptor dba);
EnsPGvindividualadaptor ensGvindividualadaptorNew(
EnsPDatabaseadaptor dba);
void ensGvindividualadaptorDel(EnsPGvindividualadaptor *Pgvia);
EnsPGvsampleadaptor ensGvindividualadaptorGetBaseadaptor(
EnsPGvindividualadaptor gvia);
EnsPDatabaseadaptor ensGvindividualadaptorGetDatabaseadaptor(
EnsPGvindividualadaptor gvia);
AjBool ensGvindividualadaptorFetchAllCoverage(
EnsPGvindividualadaptor gvia,
AjPList idlist);
AjBool ensGvindividualadaptorFetchAllDefault(
EnsPGvindividualadaptor gvia,
AjPList gvis);
AjBool ensGvindividualadaptorFetchAllDisplayable(
EnsPGvindividualadaptor gvia,
AjPList gvis);
AjBool ensGvindividualadaptorFetchAllStrains(
EnsPGvindividualadaptor gvia,
AjPList gvis);
AjBool ensGvindividualadaptorFetchAllbyDisplay(
EnsPGvindividualadaptor gvia,
EnsEGvsampleDisplay display,
AjPList gvis);
AjBool ensGvindividualadaptorFetchAllbyGvpopulation(
EnsPGvindividualadaptor gvia,
const EnsPGvpopulation gvp,
AjPList gvis);
AjBool ensGvindividualadaptorFetchAllbyName(
EnsPGvindividualadaptor gvia,
const AjPStr name,
AjPList gvis);
AjBool ensGvindividualadaptorFetchAllbyParent(
EnsPGvindividualadaptor gvia,
const EnsPGvindividual parent,
AjPList gvis);
AjBool ensGvindividualadaptorFetchAllbySynonym(
EnsPGvindividualadaptor adaptor,
const AjPStr synonym,
const AjPStr source,
AjPList individuals);
AjBool ensGvindividualadaptorFetchByIdentifier(
EnsPGvindividualadaptor gvia,
ajuint identifier,
EnsPGvindividual *Pgvi);
AjBool ensGvindividualadaptorFetchReference(
EnsPGvindividualadaptor gvia,
EnsPGvindividual *Pgvi);
/*
** End of prototype definitions
*/
AJ_END_DECLS
#endif /* !ENSGVINDIVIDUAL_H */
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