/usr/lib/emboss/include/ensassemblymapper.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.
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extern "C"
{
#endif
#ifndef ensassemblymapper_h
#define ensassemblymapper_h
#include "ensassembly.h"
#include "ensdata.h"
#include "enstable.h"
/*
** Prototype definitions
*/
/* Ensembl Generic Assembly Mapper */
EnsPGenericassemblymapper ensGenericassemblymapperNew(
EnsPAssemblymapperadaptor ama,
EnsPCoordsystem asmcs,
EnsPCoordsystem cmpcs);
EnsPGenericassemblymapper ensGenericassemblymapperNewRef(
EnsPGenericassemblymapper gam);
AjBool ensGenericassemblymapperClear(EnsPGenericassemblymapper gam);
void ensGenericassemblymapperDel(EnsPGenericassemblymapper* Pgam);
EnsPAssemblymapperadaptor ensGenericassemblymapperGetAdaptor(
const EnsPGenericassemblymapper gam);
const EnsPCoordsystem ensGenericassemblymapperGetAssembledCoordsystem(
const EnsPGenericassemblymapper gam);
const EnsPCoordsystem ensGenericassemblymapperGetComponentCoordsystem(
const EnsPGenericassemblymapper gam);
EnsPMapper ensGenericassemblymapperGetMapper(
const EnsPGenericassemblymapper gam);
ajuint ensGenericassemblymapperGetMaxPairCount(
const EnsPGenericassemblymapper gam);
ajuint ensGenericassemblymapperGetPairCount(
const EnsPGenericassemblymapper gam);
AjBool ensGenericassemblymapperSetAdaptor(EnsPGenericassemblymapper gam,
EnsPAssemblymapperadaptor ama);
AjBool ensGenericassemblymapperSetMaxPairCount(EnsPGenericassemblymapper gam,
ajuint count);
AjBool ensGenericassemblymapperRegisterAssembled(EnsPGenericassemblymapper gam,
ajuint asmsrid,
ajint chunkid);
AjBool ensGenericassemblymapperRegisterComponent(EnsPGenericassemblymapper gam,
ajuint cmpsrid);
AjBool ensGenericassemblymapperHaveRegisteredAssembled(
const EnsPGenericassemblymapper gam,
ajuint asmsrid,
ajint chunkid);
AjBool ensGenericassemblymapperHaveRegisteredComponent(
const EnsPGenericassemblymapper gam,
ajuint cmpsrid);
AjBool ensGenericassemblymapperMap(EnsPGenericassemblymapper gam,
const EnsPSeqregion sr,
ajint srstart,
ajint srend,
ajint srstrand,
AjPList mrs);
AjBool ensGenericassemblymapperFastMap(EnsPGenericassemblymapper gam,
const EnsPSeqregion sr,
ajint srstart,
ajint srend,
ajint srstrand,
AjPList mrs);
AjBool ensGenericassemblymapperRegisterAll(EnsPGenericassemblymapper gam);
/* Ensembl Chained Assembly Mapper */
EnsPChainedassemblymapper ensChainedassemblymapperNew(
EnsPAssemblymapperadaptor ama,
EnsPCoordsystem srccs,
EnsPCoordsystem midcs,
EnsPCoordsystem trgcs);
EnsPChainedassemblymapper ensChainedassemblymapperNewRef(
EnsPChainedassemblymapper cam);
void ensChainedassemblymapperDel(EnsPChainedassemblymapper *Pcam);
AjBool ensChainedassemblymapperClear(EnsPChainedassemblymapper cam);
EnsPAssemblymapperadaptor ensChainedassemblymapperGetAdaptor(
const EnsPChainedassemblymapper cam);
const EnsPCoordsystem ensChainedassemblymapperGetSourceCoordsystem(
const EnsPChainedassemblymapper cam);
const EnsPCoordsystem ensChainedassemblymapperGetMiddleCoordsystem(
const EnsPChainedassemblymapper cam);
const EnsPCoordsystem ensChainedassemblymapperGetTargetCoordsystem(
const EnsPChainedassemblymapper cam);
EnsPMapper ensChainedassemblymapperGetSourceMiddleMapper(
const EnsPChainedassemblymapper cam);
EnsPMapper ensChainedassemblymapperGetTargetMiddleMapper(
const EnsPChainedassemblymapper cam);
EnsPMapper ensChainedassemblymapperGetSourceTargetMapper(
const EnsPChainedassemblymapper cam);
EnsPMapperrangeregistry ensChainedassemblymapperGetSourceRegistry(
const EnsPChainedassemblymapper cam);
EnsPMapperrangeregistry ensChainedassemblymapperGetTargetRegistry(
const EnsPChainedassemblymapper cam);
ajuint ensChainedassemblymapperGetMaxPairCount(
const EnsPChainedassemblymapper cam);
AjBool ensChainedassemblymapperSetAdaptor(EnsPChainedassemblymapper cam,
EnsPAssemblymapperadaptor ama);
AjBool ensChainedassemblymapperSetMaxPairCount(EnsPChainedassemblymapper cam,
ajuint count);
ajuint ensChainedassemblymapperGetPairCount(
const EnsPChainedassemblymapper cam);
AjBool ensChainedassemblymapperMap(EnsPChainedassemblymapper cam,
const EnsPSeqregion sr,
ajint srstart,
ajint srend,
ajint srstrand,
const EnsPSeqregion optsr,
AjBool fastmap,
AjPList mrs);
AjBool ensChainedassemblymapperRegisterAll(EnsPChainedassemblymapper cam);
/* Ensembl Top-level Assembly Mapper */
EnsPToplevelassemblymapper ensToplevelassemblymapperNew(
EnsPAssemblymapperadaptor ama,
EnsPCoordsystem cs1,
EnsPCoordsystem cs2);
EnsPToplevelassemblymapper ensToplevelassemblymapperNewRef(
EnsPToplevelassemblymapper tlam);
void ensToplevelassemblymapperDel(EnsPToplevelassemblymapper* Ptlam);
const EnsPAssemblymapperadaptor ensToplevelassemblymapperGetAdaptor(
const EnsPToplevelassemblymapper tlam);
const EnsPCoordsystem ensToplevelassemblymapperGetAssembledCoordsystem(
const EnsPToplevelassemblymapper tlam);
const EnsPCoordsystem ensToplevelassemblymapperGetComponentCoordsystem(
const EnsPToplevelassemblymapper tlam);
AjBool ensToplevelassemblymapperSetAdaptor(
EnsPToplevelassemblymapper tlam,
EnsPAssemblymapperadaptor ama);
AjBool ensToplevelassemblymapperMap(EnsPToplevelassemblymapper tlam,
const EnsPSeqregion sr,
ajint srstart,
ajint srend,
ajint srstrand,
AjBool fastmap,
AjPList mrs);
/* Ensembl Assembly Mapper */
EnsPAssemblymapper ensAssemblymapperNew(EnsPAssemblymapperadaptor ama,
EnsPGenericassemblymapper gam,
EnsPChainedassemblymapper cam,
EnsPToplevelassemblymapper tlam);
EnsPAssemblymapper ensAssemblymapperNewRef(EnsPAssemblymapper am);
void ensAssemblymapperDel(EnsPAssemblymapper* Pam);
AjBool ensAssemblymapperMap(EnsPAssemblymapper am,
const EnsPSeqregion sr,
ajint srstart,
ajint srend,
ajint srstrand,
AjPList mrs);
AjBool ensAssemblymapperFastMap(EnsPAssemblymapper am,
const EnsPSeqregion sr,
ajint srstart,
ajint srend,
ajint srstrand,
AjPList mrs);
AjBool ensAssemblymapperMapToSeqregion(EnsPAssemblymapper am,
const EnsPSeqregion sr,
ajint srstart,
ajint srend,
ajint srstrand,
const EnsPSeqregion optsr,
AjPList mrs);
/* Ensembl Assembly Mapper Adaptor */
EnsPAssemblymapperadaptor ensRegistryGetAssemblymapperadaptor(
EnsPDatabaseadaptor dba);
EnsPAssemblymapperadaptor ensAssemblymapperadaptorNew(
EnsPDatabaseadaptor dba);
AjBool ensAssemblymapperadaptorCacheClear(EnsPAssemblymapperadaptor ama);
void ensAssemblymapperadaptorDel(EnsPAssemblymapperadaptor* Pama);
EnsPDatabaseadaptor ensAssemblymapperadaptorGetDatabaseadaptor(
const EnsPAssemblymapperadaptor ama);
EnsPAssemblymapper ensAssemblymapperadaptorFetchByCoordsystems(
EnsPAssemblymapperadaptor ama,
EnsPCoordsystem cs1,
EnsPCoordsystem cs2);
EnsPAssemblymapper ensAssemblymapperadaptorFetchBySlices(
EnsPAssemblymapperadaptor ama,
EnsPSlice slice1,
EnsPSlice slice2);
AjBool ensAssemblymapperadaptorSeqregionIdsToNames(
EnsPAssemblymapperadaptor ama,
const AjPList ids,
AjPList names);
AjBool ensAssemblymapperadaptorSeqregionNamesToIds(
EnsPAssemblymapperadaptor ama,
EnsPCoordsystem cs,
const AjPList names,
AjPList identifiers);
AjBool ensAssemblymapperadaptorRegisterAssembled(
EnsPAssemblymapperadaptor ama,
EnsPGenericassemblymapper gam,
ajuint asmsrid,
ajint regstart,
ajint regend);
AjBool ensAssemblymapperadaptorRegisterComponent(
EnsPAssemblymapperadaptor ama,
EnsPGenericassemblymapper gam,
ajuint cmpsrid);
AjBool ensAssemblymapperadaptorRegisterAll(EnsPAssemblymapperadaptor ama,
EnsPGenericassemblymapper gam);
AjBool ensAssemblymapperadaptorRegisterChained(
EnsPAssemblymapperadaptor ama,
EnsPChainedassemblymapper cam,
const AjPStr source,
ajuint srcsrid,
ajuint optsrid,
AjPList ranges);
AjBool ensAssemblymapperadaptorRegisterChainedSpecial(
EnsPAssemblymapperadaptor ama,
EnsPChainedassemblymapper cam,
const AjPStr source,
ajuint srcsrid,
ajuint optsrid,
AjPList ranges);
AjBool ensAssemblymapperadaptorRegisterAllChained(
EnsPAssemblymapperadaptor ama,
EnsPChainedassemblymapper cam);
/*
** End of prototype definitions
*/
#define MENSCHAINEDASSEMBLYMAPPERADAPTORGETASSEMBLEDCOORDSYSTEM(cam) \
ensChainedassemblymapperGetSourceCoordsystem(cam)
#define MENSCHAINEDASSEMBLYMAPPERADAPTORGETCOMPONENTCOORDSYSTEM(cam) \
ensChainedassemblymapperGetTargetCoordsystem(cam)
#define MENSCHAINEDASSEMBLYMAPPERGETMAPPER(cam) \
ensChainedassemblymapperGetSourceTargetMapper(cam)
#endif /* ensassemblymapper_h */
#ifdef __cplusplus
}
#endif
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