/usr/lib/emboss/include/ensslice.h is in emboss-lib 6.3.1-6ubuntu3.
This file is owned by root:root, with mode 0o644.
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extern "C"
{
#endif
#ifndef ensslice_h
#define ensslice_h
#include "ensassemblyexception.h"
#include "ensassemblymapper.h"
#include "enscache.h"
#include "ensmapper.h"
#include "ensseqregion.h"
#include "enstable.h"
/* EnsERepeatMaskType *********************************************************
**
** Ensembl Repeat Mask Type enumeration.
**
******************************************************************************/
typedef enum EnsORepeatMaskType
{
ensERepeatMaskTypeNULL,
ensERepeatMaskTypeNone,
ensERepeatMaskTypeSoft,
ensERepeatMaskTypeHard
} EnsERepeatMaskType;
/* @data EnsPRepeatmaskedslice ************************************************
**
** Ensembl Repeat-Masked Slice.
**
** Holds information about a masked genome sequence slice.
**
** @alias EnsSRepeatmaskedslice
** @alias EnsORepeatmaskedslice
**
** @attr Slice [EnsPSlice] Ensembl Slice.
** @attr AnalysisNames [AjPList] AJAX List of Ensembl Analysis name
** AJAX Strings
** @attr Masking [AjPTable] AJAX Table of Repeat Consensus types, classes or
** names and sequence masking types
** @attr Use [ajuint] Use counter
** @attr Padding [ajuint] Padding to alignment boundary
** @@
******************************************************************************/
typedef struct EnsSRepeatmaskedslice
{
EnsPSlice Slice;
AjPList AnalysisNames;
AjPTable Masking;
ajuint Use;
ajuint Padding;
} EnsORepeatmaskedslice;
#define EnsPRepeatmaskedslice EnsORepeatmaskedslice*
#include "ensprojectionsegment.h"
/*
** Prototype definitions
*/
/* Ensembl Slice */
EnsPSlice ensSliceNewS(EnsPSliceadaptor adaptor,
EnsPSeqregion sr,
ajint start,
ajint end,
ajint strand,
AjPStr sequence);
EnsPSlice ensSliceNew(EnsPSliceadaptor adaptor,
EnsPSeqregion sr,
ajint start,
ajint end,
ajint strand);
EnsPSlice ensSliceNewObj(EnsPSlice object);
EnsPSlice ensSliceNewRef(EnsPSlice slice);
void ensSliceDel(EnsPSlice* Pslice);
EnsPSliceadaptor ensSliceGetAdaptor(const EnsPSlice slice);
EnsPSeqregion ensSliceGetSeqregion(const EnsPSlice slice);
const AjPStr ensSliceGetSequence(const EnsPSlice slice);
ajint ensSliceGetStart(const EnsPSlice slice);
ajint ensSliceGetEnd(const EnsPSlice slice);
ajint ensSliceGetStrand(const EnsPSlice slice);
AjBool ensSliceSetAdaptor(EnsPSlice slice, EnsPSliceadaptor adaptor);
AjBool ensSliceSetSequence(EnsPSlice slice, AjPStr sequence);
AjBool ensSliceTrace(const EnsPSlice slice, ajuint level);
ajuint ensSliceGetSeqregionIdentifier(const EnsPSlice slice);
const AjPStr ensSliceGetSeqregionName(const EnsPSlice slice);
ajint ensSliceGetSeqregionLength(const EnsPSlice slice);
EnsPCoordsystem ensSliceGetCoordsystem(const EnsPSlice slice);
const AjPStr ensSliceGetCoordsystemName(const EnsPSlice slice);
const AjPStr ensSliceGetCoordsystemVersion(const EnsPSlice slice);
ajint ensSliceGetCentrePoint(const EnsPSlice slice);
ajuint ensSliceGetLength(const EnsPSlice slice);
ajulong ensSliceGetMemsize(const EnsPSlice slice);
const AjPTrn ensSliceGetTranslation(EnsPSlice slice);
AjBool ensSliceFetchName(const EnsPSlice slice, AjPStr* Pname);
int ensSliceCompareIdentifierAscending(const EnsPSlice slice1,
const EnsPSlice slice2);
AjBool ensSliceMatch(const EnsPSlice slice1, const EnsPSlice slice2);
AjBool ensSliceIsTopLevel(EnsPSlice slice, AjBool* Presult);
AjBool ensSliceFetchSequenceSeq(EnsPSlice slice, AjPSeq *Psequence);
AjBool ensSliceFetchSequenceStr(EnsPSlice slice, AjPStr *Psequence);
AjBool ensSliceFetchSubSequenceSeq(EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
AjPSeq *Psequence);
AjBool ensSliceFetchSubSequenceStr(EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
AjPStr *Psequence);
AjBool ensSliceFetchInvertedSlice(EnsPSlice slice, EnsPSlice *Pslice);
AjBool ensSliceFetchSubSlice(EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
EnsPSlice *Pslice);
AjBool ensSliceFetchExpandedSlice(const EnsPSlice slice,
ajint five,
ajint three,
AjBool force,
ajint *Pfshift,
ajint *Ptshift,
EnsPSlice *Pslice);
AjBool ensSliceProject(EnsPSlice slice,
const AjPStr csname,
const AjPStr csversion,
AjPList pss);
AjBool ensSliceProjectToSlice(EnsPSlice srcslice,
EnsPSlice trgslice,
AjPList pss);
AjBool ensSliceFetchAllAttributes(EnsPSlice slice,
const AjPStr code,
AjPList attributes);
AjBool ensSliceFetchAllRepeatfeatures(EnsPSlice slice,
const AjPStr anname,
AjPStr rctype,
AjPStr rcclass,
AjPStr rcname,
AjPList rfs);
AjBool ensSliceFetchAllSequenceEdits(EnsPSlice slice,
AjPList ses);
/* Ensembl Slice Adaptor */
EnsPSliceadaptor ensRegistryGetSliceadaptor(
EnsPDatabaseadaptor dba);
EnsPSliceadaptor ensSliceadaptorNew(
EnsPDatabaseadaptor dba);
void ensSliceadaptorDel(EnsPSliceadaptor* Padaptor);
EnsPDatabaseadaptor ensSliceadaptorGetDatabaseadaptor(
const EnsPSliceadaptor adaptor);
AjBool ensSliceadaptorCacheInsert(EnsPSliceadaptor adaptor, EnsPSlice* Pslice);
AjBool ensSliceadaptorFetchBySeqregionIdentifier(EnsPSliceadaptor adaptor,
ajuint srid,
ajint srstart,
ajint srend,
ajint srstrand,
EnsPSlice *Pslice);
AjBool ensSliceadaptorFetchByRegion(EnsPSliceadaptor adaptor,
const AjPStr csname,
const AjPStr csversion,
const AjPStr srname,
ajint srstart,
ajint srend,
ajint srstrand,
EnsPSlice *Pslice);
AjBool ensSliceadaptorFetchByName(EnsPSliceadaptor adaptor,
const AjPStr name,
EnsPSlice *Pslice);
AjBool ensSliceadaptorFetchBySlice(EnsPSliceadaptor adaptor,
EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
EnsPSlice *Pslice);
AjBool ensSliceadaptorFetchByFeature(EnsPSliceadaptor adaptor,
const EnsPFeature feature,
ajint flank,
EnsPSlice *Pslice);
AjBool ensSliceadaptorFetchNormalisedSliceProjection(EnsPSliceadaptor adaptor,
EnsPSlice slice,
AjPList pss);
AjBool ensSliceadaptorFetchAll(EnsPSliceadaptor adaptor,
const AjPStr csname,
const AjPStr csversion,
AjBool nonreference,
AjBool duplicates,
AjPList slices);
/* Ensembl Repeat-Masked Slice */
EnsPRepeatmaskedslice ensRepeatmaskedsliceNew(EnsPSlice slice,
AjPList annames,
AjPTable masking);
EnsPRepeatmaskedslice ensRepeatmaskedsliceNewObj(
EnsPRepeatmaskedslice object);
EnsPRepeatmaskedslice ensRepeatmaskedsliceNewRef(
EnsPRepeatmaskedslice rmslice);
void ensRepeatmaskedsliceDel(EnsPRepeatmaskedslice* Prmslice);
AjBool ensRepeatmaskedsliceFetchSequenceSeq(EnsPRepeatmaskedslice rmslice,
EnsERepeatMaskType mtype,
AjPSeq *Psequence);
AjBool ensRepeatmaskedsliceFetchSequenceStr(EnsPRepeatmaskedslice rmslice,
EnsERepeatMaskType mtype,
AjPStr *Psequence);
/*
** End of prototype definitions
*/
#endif /* ensslice_h */
#ifdef __cplusplus
}
#endif
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