/usr/lib/emboss/include/ensqcsequence.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 | #ifdef __cplusplus
extern "C"
{
#endif
#ifndef ensqcsequence_h
#define ensqcsequence_h
#include "ensqcdatabase.h"
/* @data EnsPQcsequenceadaptor ************************************************
**
** Ensembl QC Sequence Adaptor
**
** @alias EnsSQcsequenceadaptor
** @alias EnsOQcsequenceadaptor
**
** @attr Adaptor [EnsPBaseadaptor] Ensembl Base Adaptor
** @attr CacheByIdentifier [AjPTable] Identifier cache
** @attr CacheByName [AjPTable] Name cache
** @@
** FIXME: Should this also have a CacheByAccessionVersion???
******************************************************************************/
typedef struct EnsSQcsequenceadaptor
{
EnsPBaseadaptor Adaptor;
AjPTable CacheByIdentifier;
AjPTable CacheByName;
} EnsOQcsequenceadaptor;
#define EnsPQcsequenceadaptor EnsOQcsequenceadaptor*
/* @data EnsPQcsequence *******************************************************
**
** Ensembl QC Sequence
**
** @alias EnsSQcsequence
** @alias EnsOQcsequence
**
** @attr Use [ajuint] Use counter
** @cc Bio::EnsEMBL::Storable
** @attr Identifier [ajuint] SQL database-internal identifier
** @attr Adaptor [EnsPQcsequenceadaptor] Ensembl Sequence Adaptor
** @cc Bio::EnsEMBL::QC::Sequence
** @cc 'sequence' SQL table
** @attr Qcdatabase [EnsPQcdatabase] Ensembl QC Database
** @attr Name [AjPStr] Name
** @attr Accession [AjPStr] Accession
** @attr Description [AjPStr] Description
** @attr Type [AjPStr] Type
** @attr Version [ajuint] Version
** @attr Length [ajuint] Length
** @attr CDSStart [ajuint] Coding sequence start
** @attr CDSEnd [ajuint] Coding sequence end
** @attr CDSStrand [ajint] Coding sequence strand
** @attr PolyA [ajuint] Poly A+ tail length
** @@
******************************************************************************/
typedef struct EnsSQcsequence
{
ajuint Use;
ajuint Identifier;
EnsPQcsequenceadaptor Adaptor;
EnsPQcdatabase Qcdatabase;
AjPStr Name;
AjPStr Accession;
AjPStr Description;
AjPStr Type;
ajuint Version;
ajuint Length;
ajuint CDSStart;
ajuint CDSEnd;
ajint CDSStrand;
ajuint PolyA;
} EnsOQcsequence;
#define EnsPQcsequence EnsOQcsequence*
/*
** Prototype definitions
*/
/* Ensembl Quality Check Sequence */
EnsPQcsequence ensQcsequenceNew(EnsPQcsequenceadaptor adaptor,
ajuint identifier,
EnsPQcdatabase qcdb,
AjPStr name,
AjPStr accession,
ajuint version,
AjPStr type,
ajuint length,
ajuint cdsstart,
ajuint cdsend,
ajint cdsstrand,
ajuint polya,
AjPStr description);
EnsPQcsequence ensQcsequenceNewObj(const EnsPQcsequence object);
EnsPQcsequence ensQcsequenceNewRef(EnsPQcsequence qcs);
void ensQcsequenceDel(EnsPQcsequence* Pqcs);
EnsPQcsequenceadaptor ensQcsequenceGetAdaptor(const EnsPQcsequence qcs);
ajuint ensQcsequenceGetIdentifier(const EnsPQcsequence qcs);
EnsPQcdatabase ensQcsequenceGetQcdatabase(const EnsPQcsequence qcs);
AjPStr ensQcsequenceGetName(const EnsPQcsequence qcs);
AjPStr ensQcsequenceGetAccession(const EnsPQcsequence qcs);
ajuint ensQcsequenceGetVersion(const EnsPQcsequence qcs);
AjPStr ensQcsequenceGetType(const EnsPQcsequence qcs);
ajuint ensQcsequenceGetLength(const EnsPQcsequence qcs);
ajuint ensQcsequenceGetCDSStart(const EnsPQcsequence qcs);
ajuint ensQcsequenceGetCDSEnd(const EnsPQcsequence qcs);
ajint ensQcsequenceGetCDSStrand(const EnsPQcsequence qcs);
ajuint ensQcsequenceGetPolyA(const EnsPQcsequence qcs);
AjPStr ensQcsequenceGetDescription(const EnsPQcsequence qcs);
AjBool ensQcsequenceSetAdaptor(EnsPQcsequence qcs, EnsPQcsequenceadaptor qcsa);
AjBool ensQcsequenceSetIdentifier(EnsPQcsequence qcs, ajuint identifier);
AjBool ensQcsequenceSetQcdatabase(EnsPQcsequence qcs, EnsPQcdatabase qcdb);
AjBool ensQcsequenceSetName(EnsPQcsequence qcs, AjPStr name);
AjBool ensQcsequenceSetAccession(EnsPQcsequence qcs, AjPStr accession);
AjBool ensQcsequenceSetVersion(EnsPQcsequence qcs, ajuint version);
AjBool ensQcsequenceSetType(EnsPQcsequence qcs, AjPStr type);
AjBool ensQcsequenceSetLength(EnsPQcsequence qcs, ajuint length);
AjBool ensQcsequenceSetCDSStart(EnsPQcsequence qcs, ajuint cdsstart);
AjBool ensQcsequenceSetCDSEnd(EnsPQcsequence qcs, ajuint cdsend);
AjBool ensQcsequenceSetCDSStrand(EnsPQcsequence qcs, ajint cdsstrand);
AjBool ensQcsequenceSetPolyA(EnsPQcsequence qcs, ajuint polya);
AjBool ensQcsequenceSetDescription(EnsPQcsequence qcs, AjPStr description);
ajulong ensQcsequenceGetMemsize(const EnsPQcsequence qcs);
AjBool ensQcsequenceTrace(const EnsPQcsequence qcs, ajuint level);
AjBool ensQcsequenceMatch(const EnsPQcsequence qcs1,
const EnsPQcsequence qcs2);
ajuint ensQcsequenceGetQcdatabaseIdentifier(const EnsPQcsequence qcs);
AjBool ensHTMLEncodeSGMLID(AjPStr *Pstr);
AjBool ensHTMLEncodeEntities(AjPStr *Pstr);
AjBool ensQcsequenceFetchExternalURL(const EnsPQcsequence qcs, AjPStr *Pstr);
AjBool ensQcsequenceFetchExternalAnchor(const EnsPQcsequence qcs,
AjPStr *Pstr,
AjBool htmlid);
AjBool ensQcsequenceFetchInternalAnchor(const EnsPQcsequence qcs,
AjPStr *Pstr);
/* Ensembl Quality Check Sequence Adaptor */
EnsPQcsequenceadaptor ensRegistryGetQcsequenceadaptor(
EnsPDatabaseadaptor dba);
EnsPQcsequenceadaptor ensQcsequenceadaptorNew(
EnsPDatabaseadaptor dba);
void ensQcsequenceadaptorDel(EnsPQcsequenceadaptor* Pqcsa);
AjBool ensQcsequenceadaptorFetchByIdentifier(EnsPQcsequenceadaptor adaptor,
ajuint identifier,
EnsPQcsequence *Pqcs);
AjBool ensQcsequenceadaptorFetchByAccession(EnsPQcsequenceadaptor qcsa,
ajuint qcdbid,
const AjPStr accession,
EnsPQcsequence *Pqcs);
AjBool ensQcsequenceadaptorFetchByAccessionVersion(EnsPQcsequenceadaptor qcsa,
ajuint qcdbid,
const AjPStr accession,
ajuint version,
EnsPQcsequence *Pqcs);
AjBool ensQcsequenceadaptorFetchByName(EnsPQcsequenceadaptor qcsa,
ajuint qcdbid,
const AjPStr name,
EnsPQcsequence *Pqcs);
AjBool ensQcsequenceadaptorFetchAllByQcdatabase(EnsPQcsequenceadaptor qcsa,
const EnsPQcdatabase qcdb,
AjPList qcss);
AjBool ensQcsequenceadaptorStore(EnsPQcsequenceadaptor qcsa,
EnsPQcsequence qcs);
AjBool ensQcsequenceadaptorUpdate(EnsPQcsequenceadaptor qcsa,
const EnsPQcsequence qcs);
AjBool ensQcsequenceadaptorDelete(EnsPQcsequenceadaptor qcsa,
EnsPQcsequence qcs);
/*
** End of prototype definitions
*/
#endif /* ensqcsequence_h */
#ifdef __cplusplus
}
#endif
|