/usr/lib/emboss/include/ensdatabaseadaptor.h is in emboss-lib 6.3.1-6ubuntu3.
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 | #ifdef __cplusplus
extern "C"
{
#endif
#ifndef ensdatabaseadaptor_h
#define ensdatabaseadaptor_h
#include "ensdatabaseconnection.h"
/* EnsMDatabaseadaptorGroups **************************************************
**
** Number of Ensembl Database Adaptor groups.
**
** The number of Ensembl Database Adaptor groups has to correlate with the
** EnsEDatabaseadaptorGroup enumeration list and the
** static const char *databaseadaptorGroup[] array. It is used by the
** ensregistry.[ch] module.
**
******************************************************************************/
#define EnsMDatabaseadaptorGroups 17
/* EnsEDatabaseadaptorGroup ***************************************************
**
** Ensembl Database Adaptor group enumeration.
**
******************************************************************************/
typedef enum EnsODatabaseadaptorGroup
{
ensEDatabaseadaptorGroupNULL,
ensEDatabaseadaptorGroupCore,
ensEDatabaseadaptorGroupVega,
ensEDatabaseadaptorGroupOtherFeatures,
ensEDatabaseadaptorGroupCopyDNA,
ensEDatabaseadaptorGroupGeneticVariation,
ensEDatabaseadaptorGroupFunctionalGenomics,
ensEDatabaseadaptorGroupComparativeGenomics,
ensEDatabaseadaptorGroupOntology,
ensEDatabaseadaptorGroupQualityCheck,
ensEDatabaseadaptorGroupPipeline,
ensEDatabaseadaptorGroupHive,
ensEDatabaseadaptorGroupCoreExpressionEST,
ensEDatabaseadaptorGroupCoreExpressionGNF,
ensEDatabaseadaptorGroupAncestral,
ensEDatabaseadaptorGroupWebsite,
ensEDatabaseadaptorGroupProduction
} EnsEDatabaseadaptorGroup;
/* @data EnsPDatabaseadaptor **************************************************
**
** Ensembl Database Adaptor.
**
** Holds the Ensembl Database Group, the species name and the Ensembl
** Database Connection object connected to this SQL database.
**
** @alias EnsSDatabaseadaptor
** @alias EnsODatabaseadaptor
**
** @alias EnsPAttributeadaptor
** @alias EnsPDitagadaptor
** @alias EnsPRepeatconsensusadaptor
** @alias EnsPGvalleleadaptor
** @alias EnsPGvgenotypeadaptor
** @alias EnsPGvvariationadaptor
**
** @attr Databaseconnection [EnsPDatabaseconnection] Ensembl Database
** Connection
** @attr Species [AjPStr] Species
** @attr SpeciesNames [AjPList] AJAX List of species name AJAX Strings
** @attr Group [EnsEDatabaseadaptorGroup] Group
** @attr MultiSpecies [AjBool] Multi-species database
** @attr Identifier [ajuint] Species identifier, defaults to 1
** @attr Padding [ajuint] Padding to alignment boundary
** @@
******************************************************************************/
typedef struct EnsSDatabaseadaptor
{
EnsPDatabaseconnection Databaseconnection;
AjPStr Species;
AjPList SpeciesNames;
EnsEDatabaseadaptorGroup Group;
AjBool MultiSpecies;
ajuint Identifier;
ajuint Padding;
} EnsODatabaseadaptor;
#define EnsPDatabaseadaptor EnsODatabaseadaptor*
/*
** Prototype definitions
*/
/* Ensembl Database Adaptor */
EnsPDatabaseadaptor ensRegistryGetDatabaseadaptor(
EnsEDatabaseadaptorGroup group,
const AjPStr alias);
EnsPDatabaseadaptor ensRegistryGetReferenceadaptor(EnsPDatabaseadaptor dba);
EnsPDatabaseadaptor ensDatabaseadaptorNew(EnsPDatabaseconnection dbc,
AjPStr database,
AjPStr species,
EnsEDatabaseadaptorGroup group,
AjBool multi,
ajuint identifier);
void ensDatabaseadaptorDel(EnsPDatabaseadaptor* Pdba);
EnsPDatabaseconnection ensDatabaseadaptorGetDatabaseconnection(
const EnsPDatabaseadaptor dba);
AjPStr ensDatabaseadaptorGetSpecies(const EnsPDatabaseadaptor dba);
EnsEDatabaseadaptorGroup ensDatabaseadaptorGetGroup(
const EnsPDatabaseadaptor dba);
AjBool ensDatabaseadaptorGetMultiSpecies(const EnsPDatabaseadaptor dba);
ajuint ensDatabaseadaptorGetIdentifier(const EnsPDatabaseadaptor dba);
AjBool ensDatabaseadaptorSetDatabaseconnection(EnsPDatabaseadaptor dba,
EnsPDatabaseconnection dbc);
AjBool ensDatabaseadaptorSetSpecies(EnsPDatabaseadaptor dba, AjPStr species);
AjBool ensDatabaseadaptorSetGroup(EnsPDatabaseadaptor dba,
EnsEDatabaseadaptorGroup group);
AjBool ensDatabaseadaptorSetMultiSpecies(EnsPDatabaseadaptor dba,
AjBool multi);
AjBool ensDatabaseadaptorSetIdentifier(EnsPDatabaseadaptor dba,
ajuint identifier);
EnsEDatabaseadaptorGroup ensDatabaseadaptorGroupFromStr(const AjPStr group);
const char *ensDatabaseadaptorGroupToChar(EnsEDatabaseadaptorGroup group);
AjBool ensDatabaseadaptorMatch(const EnsPDatabaseadaptor dba1,
const EnsPDatabaseadaptor dba2);
AjBool ensDatabaseadaptorMatchComponents(const EnsPDatabaseadaptor dba,
const EnsPDatabaseconnection dbc,
const AjPStr species,
EnsEDatabaseadaptorGroup group,
AjBool multi,
ajuint identifier);
AjPSqlstatement ensDatabaseadaptorSqlstatementNew(EnsPDatabaseadaptor dba,
const AjPStr statement);
AjBool ensDatabaseadaptorSqlstatementDel(EnsPDatabaseadaptor dba,
AjPSqlstatement *Psqls);
AjBool ensDatabaseadaptorDisconnect(EnsPDatabaseadaptor dba);
AjBool ensDatabaseadaptorEscapeC(EnsPDatabaseadaptor dba,
char **Ptxt,
const AjPStr str);
AjBool ensDatabaseadaptorEscapeS(EnsPDatabaseadaptor dba,
AjPStr *Pstr,
const AjPStr str);
AjBool ensDatabaseadaptorTrace(const EnsPDatabaseadaptor dba, ajuint level);
AjBool ensDatabaseadaptorGetSchemaBuild(const EnsPDatabaseadaptor dba,
AjPStr *Pbuild);
const AjPList ensDatabaseadaptorGetAllSpeciesNames(EnsPDatabaseadaptor dba);
/*
** End of prototype definitions
*/
#endif /* ensdatabaseadaptor_h */
#ifdef __cplusplus
}
#endif
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