/usr/lib/emboss/include/ensbaseadaptor.h is in emboss-lib 6.6.0-1.
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 | /* @include ensbaseadaptor ****************************************************
**
** Ensembl Base Adaptor functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.24 $
** @modified 2009 by Alan Bleasby for incorporation into EMBOSS core
** @modified $Date: 2013/02/17 13:03:48 $ 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 ENSBASEADAPTOR_H
#define ENSBASEADAPTOR_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ensassemblymapper.h"
#include "ensdata.h"
#include "ensslice.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
extern const ajuint ensKBaseadaptorMaximumIdentifiers;
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
/* Ensembl Base Adaptor */
EnsPBaseadaptor ensBaseadaptorNew(
EnsPDatabaseadaptor dba,
const char *const *Ptablenames,
const char *const *Pcolumnnames,
const EnsPBaseadaptorLeftjoin leftjoins,
const char *defaultcondition,
const char *finalcondition,
AjBool (*Fstatement) (EnsPBaseadaptor ba,
const AjPStr statement,
EnsPAssemblymapper am,
EnsPSlice slice,
AjPList objects));
void ensBaseadaptorDel(EnsPBaseadaptor *Pba);
const char *const *ensBaseadaptorGetColumnnames(const EnsPBaseadaptor ba);
EnsPDatabaseadaptor ensBaseadaptorGetDatabaseadaptor(const EnsPBaseadaptor ba);
const char *const *ensBaseadaptorGetTablenames(const EnsPBaseadaptor ba);
AjBool ensBaseadaptorSetColumnnames(EnsPBaseadaptor ba,
const char *const *Pcolumnnames);
AjBool ensBaseadaptorSetDefaultcondition(EnsPBaseadaptor ba,
const char *defaultcondition);
AjBool ensBaseadaptorSetFinalcondition(EnsPBaseadaptor ba,
const char *finalcondition);
AjBool ensBaseadaptorSetTablenames(EnsPBaseadaptor ba,
const char *const *Ptablenames);
AjBool ensBaseadaptorEscapeC(EnsPBaseadaptor ba,
char **Ptxt,
const AjPStr str);
AjBool ensBaseadaptorEscapeS(EnsPBaseadaptor ba,
AjPStr *Pstr,
const AjPStr str);
AjBool ensBaseadaptorGetMultispecies(const EnsPBaseadaptor ba);
const char *ensBaseadaptorGetPrimarytable(const EnsPBaseadaptor ba);
ajuint ensBaseadaptorGetSpeciesidentifier(const EnsPBaseadaptor ba);
AjBool ensBaseadaptorCountAll(
EnsPBaseadaptor ba,
ajuint *Pcount);
AjBool ensBaseadaptorCountAllbyConstraint(
EnsPBaseadaptor ba,
const AjPStr constraint,
ajuint *Pcount);
AjBool ensBaseadaptorFetchAll(
EnsPBaseadaptor ba,
AjPList objects);
AjBool ensBaseadaptorFetchAllbyConstraint(
EnsPBaseadaptor ba,
const AjPStr constraint,
EnsPAssemblymapper am,
EnsPSlice slice,
AjPList objects);
AjBool ensBaseadaptorFetchAllbyIdentifiers(
EnsPBaseadaptor ba,
EnsPSlice slice,
ajuint (*FobjectGetIdentifier) (const void *object),
AjPTable objects);
AjBool ensBaseadaptorFetchByIdentifier(
EnsPBaseadaptor ba,
ajuint identifier,
void **Pobject);
AjBool ensBaseadaptorRetrieveAllIdentifiers(
EnsPBaseadaptor ba,
const AjPStr tablename,
const AjPStr columnname,
AjPList identifiers);
AjBool ensBaseadaptorRetrieveAllStrings(
EnsPBaseadaptor ba,
const AjPStr tablename,
const AjPStr columnname,
AjPList strings);
AjBool ensBaseadaptorRetrieveFeature(
EnsPBaseadaptor ba,
ajuint analysisid,
ajuint srid,
ajuint srstart,
ajuint srend,
ajint srstrand,
EnsPAssemblymapper am,
EnsPSlice slice,
EnsPFeature *Pfeature);
/*
** End of prototype definitions
*/
AJ_END_DECLS
#endif /* !ENSBASEADAPTOR_H */
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