/usr/lib/emboss/include/ensexon.h is in emboss-lib 6.3.1-6ubuntu3.
This file is owned by root:root, with mode 0o644.
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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 | #ifdef __cplusplus
extern "C"
{
#endif
#ifndef ensexon_h
#define ensexon_h
#include "ensdata.h"
#include "ensfeature.h"
/*
** Prototype definitions
*/
/* Ensembl Exon */
EnsPExon ensExonNew(EnsPExonadaptor ea,
ajuint identifier,
EnsPFeature feature,
ajint sphase,
ajint ephase,
AjBool current,
AjBool constitutive,
AjPStr stableid,
ajuint version,
AjPStr cdate,
AjPStr mdate);
EnsPExon ensExonNewObj(const EnsPExon object);
EnsPExon ensExonNewRef(EnsPExon exon);
void ensExonDel(EnsPExon* Pexon);
EnsPExonadaptor ensExonGetAdaptor(const EnsPExon exon);
ajuint ensExonGetIdentifier(const EnsPExon exon);
EnsPFeature ensExonGetFeature(const EnsPExon exon);
ajint ensExonGetStartPhase(const EnsPExon exon);
ajint ensExonGetEndPhase(const EnsPExon exon);
AjBool ensExonGetCurrent(const EnsPExon exon);
AjBool ensExonGetConstitutive(const EnsPExon exon);
AjPStr ensExonGetStableIdentifier(const EnsPExon exon);
ajuint ensExonGetVersion(const EnsPExon exon);
AjPStr ensExonGetCreationDate(const EnsPExon exon);
AjPStr ensExonGetModificationDate(const EnsPExon exon);
const AjPList ensExonGetSupportingfeatures(EnsPExon exon);
AjBool ensExonSetAdaptor(EnsPExon exon, EnsPExonadaptor ea);
AjBool ensExonSetIdentifier(EnsPExon exon, ajuint identifier);
AjBool ensExonSetFeature(EnsPExon exon, EnsPFeature feature);
AjBool ensExonSetStartPhase(EnsPExon exon, ajint sphase);
AjBool ensExonSetEndPhase(EnsPExon exon, ajint ephase);
AjBool ensExonSetCurrent(EnsPExon exon, AjBool current);
AjBool ensExonSetConstitutive(EnsPExon exon, AjBool constitutive);
AjBool ensExonSetStableIdentifier(EnsPExon exon, AjPStr stableid);
AjBool ensExonSetVersion(EnsPExon exon, ajuint version);
AjBool ensExonSetCreationDate(EnsPExon exon, AjPStr cdate);
AjBool ensExonSetModificationDate(EnsPExon exon, AjPStr mdate);
AjBool ensExonTrace(const EnsPExon exon, ajuint level);
ajint ensExonGetFrame(const EnsPExon exon);
ajulong ensExonGetMemsize(const EnsPExon exon);
EnsPExon ensExonTransform(EnsPExon exon, const AjPStr csname,
const AjPStr csversion);
EnsPExon ensExonTransfer(EnsPExon exon, EnsPSlice slice);
AjBool ensExonFetchDisplayIdentifier(const EnsPExon exon, AjPStr* Pidentifier);
AjBool ensExonFetchSequenceStr(EnsPExon exon, AjPStr* Psequence);
AjBool ensExonFetchSequenceSeq(EnsPExon exon, AjPSeq* Psequence);
ajuint ensExonGetTranscriptStart(EnsPExon exon, EnsPTranscript transcript);
ajuint ensExonGetTranscriptEnd(EnsPExon exon, EnsPTranscript transcript);
ajuint ensExonGetTranscriptCodingStart(EnsPExon exon,
EnsPTranscript transcript);
ajuint ensExonGetTranscriptCodingEnd(EnsPExon exon, EnsPTranscript transcript);
ajuint ensExonGetSliceCodingStart(EnsPExon exon, EnsPTranscript transcript);
ajuint ensExonGetSliceCodingEnd(EnsPExon exon, EnsPTranscript transcript);
AjBool ensExonSortByStartAscending(AjPList exons);
AjBool ensExonSortByStartDescending(AjPList exons);
/* Ensembl Exon Adaptor */
EnsPExonadaptor ensRegistryGetExonadaptor(
EnsPDatabaseadaptor dba);
EnsPExonadaptor ensExonadaptorNew(
EnsPDatabaseadaptor dba);
void ensExonadaptorDel(EnsPExonadaptor *Pea);
EnsPFeatureadaptor ensExonadaptorGetFeatureadaptor(
const EnsPExonadaptor ea);
EnsPDatabaseadaptor ensExonadaptorGetDatabaseadaptor(
const EnsPExonadaptor ea);
AjBool ensExonadaptorFetchAll(const EnsPExonadaptor ea, AjPList exons);
AjBool ensExonadaptorFetchAllBySlice(const EnsPExonadaptor ea,
EnsPSlice slice,
AjPList exons);
AjBool ensExonadaptorFetchAllBySliceConstraint(const EnsPExonadaptor ea,
EnsPSlice slice,
const AjPStr constraint,
AjPList exons);
AjBool ensExonadaptorFetchByIdentifier(const EnsPExonadaptor ea,
ajuint identifier,
EnsPExon *Pexon);
AjBool ensExonadaptorFetchByStableIdentifier(const EnsPExonadaptor ea,
const AjPStr stableid,
ajuint version,
EnsPExon *Pexon);
AjBool ensExonadaptorFetchAllByStableIdentifier(const EnsPExonadaptor ea,
const AjPStr stableid,
AjPList exons);
AjBool ensExonadaptorFetchAllByTranscript(const EnsPExonadaptor ea,
const EnsPTranscript transcript,
AjPList exons);
AjBool ensExonadaptorFetchAllIdentifiers(const EnsPExonadaptor ea,
AjPList identifiers);
AjBool ensExonadaptorFetchAllStableIdentifiers(const EnsPExonadaptor ea,
AjPList identifiers);
/* Ensembl Supporting Feature Adaptor */
AjBool ensSupportingfeatureadaptorFetchAllByExon(EnsPDatabaseadaptor dba,
EnsPExon exon,
AjPList bafs);
/*
** End of prototype definitions
*/
#endif /* ensexon_h */
#ifdef __cplusplus
}
#endif
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