/usr/lib/emboss/include/ensslice.h is in emboss-lib 6.6.0+dfsg-1.
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**
** Ensembl Slice functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.28 $
** @modified 2009 by Alan Bleasby for incorporation into EMBOSS core
** @modified $Date: 2012/02/20 22:15:10 $ by $Author: mks $
** @@
**
** This library is free software; you can redistribute it and/or
** modify it under the terms of the GNU Lesser General Public
** License as published by the Free Software Foundation; either
** version 2.1 of the License, or (at your option) any later version.
**
** This library is distributed in the hope that it will be useful,
** but WITHOUT ANY WARRANTY; without even the implied warranty of
** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
** Lesser General Public License for more details.
**
** You should have received a copy of the GNU Lesser General Public
** License along with this library; if not, write to the Free Software
** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
** MA 02110-1301, USA.
**
******************************************************************************/
#ifndef ENSSLICE_H
#define ENSSLICE_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ensseqregion.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* @enum EnsERepeatMaskType ***************************************************
**
** Ensembl Repeat Mask Type enumeration
**
** @value ensERepeatMaskTypeNULL Null
** @value ensERepeatMaskTypeNone None
** @value ensERepeatMaskTypeSoft Soft-masking
** @value ensERepeatMaskTypeHard Hard-masking
** @@
******************************************************************************/
typedef enum EnsORepeatMaskType
{
ensERepeatMaskTypeNULL,
ensERepeatMaskTypeNone,
ensERepeatMaskTypeSoft,
ensERepeatMaskTypeHard
} EnsERepeatMaskType;
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* @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 AJAX String objects
** (Ensembl Analysis names)
** @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*
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
/* Ensembl Slice */
EnsPSlice ensSliceNewCpy(const EnsPSlice slice);
EnsPSlice ensSliceNewIni(EnsPSliceadaptor sla,
EnsPSeqregion sr,
ajint start,
ajint end,
ajint strand);
EnsPSlice ensSliceNewRef(EnsPSlice slice);
EnsPSlice ensSliceNewSeq(EnsPSliceadaptor sla,
EnsPSeqregion sr,
ajint start,
ajint end,
ajint strand,
AjPStr sequence);
void ensSliceDel(EnsPSlice *Pslice);
EnsPSliceadaptor ensSliceGetAdaptor(const EnsPSlice slice);
ajint ensSliceGetEnd(const EnsPSlice slice);
EnsPSeqregion ensSliceGetSeqregion(const EnsPSlice slice);
const AjPStr ensSliceGetSequence(const EnsPSlice slice);
ajint ensSliceGetStart(const EnsPSlice slice);
ajint ensSliceGetStrand(const EnsPSlice slice);
EnsESliceTopology ensSliceLoadTopology(EnsPSlice slice);
AjBool ensSliceSetAdaptor(EnsPSlice slice, EnsPSliceadaptor sla);
AjBool ensSliceSetSequence(EnsPSlice slice, AjPStr sequence);
AjBool ensSliceSetTopology(EnsPSlice slice, EnsESliceTopology sltp);
AjBool ensSliceTrace(const EnsPSlice slice, ajuint level);
const AjPStr ensSliceGetCoordsystemName(const EnsPSlice slice);
EnsPCoordsystem ensSliceGetCoordsystemObject(const EnsPSlice slice);
const AjPStr ensSliceGetCoordsystemVersion(const EnsPSlice slice);
ajuint ensSliceGetSeqregionIdentifier(const EnsPSlice slice);
ajint ensSliceGetSeqregionLength(const EnsPSlice slice);
const AjPStr ensSliceGetSeqregionName(const EnsPSlice slice);
const AjPTrn ensSliceGetTranslation(EnsPSlice slice);
ajint ensSliceCalculateCentrepoint(EnsPSlice slice);
ajuint ensSliceCalculateLength(EnsPSlice slice);
size_t ensSliceCalculateMemsize(const EnsPSlice slice);
ajuint ensSliceCalculateRegion(EnsPSlice slice, ajint start, ajint end);
AjBool ensSliceFetchAllAttributes(EnsPSlice slice,
const AjPStr code,
AjPList attributes);
AjBool ensSliceFetchAllRepeatfeatures(EnsPSlice slice,
const AjPStr anname,
const AjPStr rctype,
const AjPStr rcclass,
const AjPStr rcname,
AjPList rfs);
AjBool ensSliceFetchAllSequenceedits(EnsPSlice slice,
AjPList ses);
AjBool ensSliceFetchName(const EnsPSlice slice, AjPStr *Pname);
AjBool ensSliceFetchSequenceAllSeq(EnsPSlice slice, AjPSeq *Psequence);
AjBool ensSliceFetchSequenceAllStr(EnsPSlice slice, AjPStr *Psequence);
AjBool ensSliceFetchSequenceSubSeq(EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
AjPSeq *Psequence);
AjBool ensSliceFetchSequenceSubStr(EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
AjPStr *Psequence);
AjBool ensSliceFetchSliceinverted(EnsPSlice slice,
EnsPSlice *Pslice);
AjBool ensSliceFetchSlicesub(EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
EnsPSlice *Pslice);
AjBool ensSliceFetchSliceexpanded(EnsPSlice slice,
ajint five,
ajint three,
AjBool force,
ajint *Pfshift,
ajint *Ptshift,
EnsPSlice *Pslice);
int ensSliceCompareIdentifierAscending(const EnsPSlice slice1,
const EnsPSlice slice2);
AjBool ensSliceMatch(const EnsPSlice slice1, const EnsPSlice slice2);
AjBool ensSliceSimilarity(const EnsPSlice slice1, const EnsPSlice slice2);
AjBool ensSliceIsCircular(EnsPSlice slice, AjBool *Presult);
AjBool ensSliceIsNonreference(EnsPSlice slice, AjBool *Presult);
AjBool ensSliceIsToplevel(EnsPSlice slice, AjBool *Presult);
AjBool ensSliceProject(EnsPSlice slice,
const AjPStr csname,
const AjPStr csversion,
AjPList pss);
AjBool ensSliceProjectslice(EnsPSlice srcslice,
EnsPSlice trgslice,
AjPList pss);
EnsESliceType ensSliceTypeFromSeqregion(EnsPSeqregion sr);
EnsESliceType ensSliceTypeFromStr(const AjPStr type);
const char *ensSliceTypeToChar(EnsESliceType ste);
AjBool ensListSliceRemoveDuplications(AjPList slices);
AjBool ensListSliceSortIdentifierAscending(AjPList slices);
AjBool ensListSliceSortIdentifierDescending(AjPList slices);
AjBool ensListSliceSortNameAscending(AjPList slices);
AjBool ensListSliceSortNameDescending(AjPList slices);
/* Ensembl Slice Adaptor */
EnsPSliceadaptor ensRegistryGetSliceadaptor(
EnsPDatabaseadaptor dba);
EnsPSliceadaptor ensSliceadaptorNew(
EnsPDatabaseadaptor dba);
void ensSliceadaptorDel(EnsPSliceadaptor *Psla);
EnsPDatabaseadaptor ensSliceadaptorGetDatabaseadaptor(
EnsPSliceadaptor sla);
AjBool ensSliceadaptorCacheInsert(EnsPSliceadaptor sla, EnsPSlice *Pslice);
AjBool ensSliceadaptorFetchAll(EnsPSliceadaptor sla,
const AjPStr csname,
const AjPStr csversion,
AjBool nonreference,
AjBool duplicates,
AjBool lrg,
AjPList slices);
AjBool ensSliceadaptorFetchAllbyRegionunique(EnsPSliceadaptor sla,
const AjPStr csname,
const AjPStr csversion,
const AjPStr srname,
ajint srstart,
ajint srend,
ajint srstrand,
AjPList slices);
AjBool ensSliceadaptorFetchByFeature(EnsPSliceadaptor sla,
const EnsPFeature feature,
ajint flank,
EnsPSlice *Pslice);
AjBool ensSliceadaptorFetchByLocation(EnsPSliceadaptor sla,
const AjPStr location,
EnsPSlice *Pslice);
AjBool ensSliceadaptorFetchByMapperresult(EnsPSliceadaptor sla,
const EnsPMapperresult mr,
EnsPSlice *Pslice);
AjBool ensSliceadaptorFetchByName(EnsPSliceadaptor sla,
const AjPStr name,
EnsPSlice *Pslice);
AjBool ensSliceadaptorFetchByRegion(EnsPSliceadaptor sla,
const AjPStr csname,
const AjPStr csversion,
const AjPStr srname,
ajint srstart,
ajint srend,
ajint srstrand,
EnsPSlice *Pslice);
AjBool ensSliceadaptorFetchBySeqregionIdentifier(EnsPSliceadaptor sla,
ajuint srid,
ajint srstart,
ajint srend,
ajint srstrand,
EnsPSlice *Pslice);
AjBool ensSliceadaptorFetchBySeqregionName(EnsPSliceadaptor sla,
const AjPStr csname,
const AjPStr csversion,
const AjPStr srname,
EnsPSlice *Pslice);
AjBool ensSliceadaptorFetchBySlice(EnsPSliceadaptor sla,
EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
EnsPSlice *Pslice);
AjBool ensSliceadaptorRetrieveNormalisedprojection(EnsPSliceadaptor sla,
EnsPSlice slice,
AjPList pss);
/* Ensembl Repeat-Masked Slice */
EnsPRepeatmaskedslice ensRepeatmaskedsliceNewCpy(
const EnsPRepeatmaskedslice rmslice);
EnsPRepeatmaskedslice ensRepeatmaskedsliceNewIni(EnsPSlice slice,
AjPList annames,
AjPTable masking);
EnsPRepeatmaskedslice ensRepeatmaskedsliceNewRef(
EnsPRepeatmaskedslice rmslice);
void ensRepeatmaskedsliceDel(EnsPRepeatmaskedslice *Prmslice);
AjBool ensRepeatmaskedsliceTrace(const EnsPRepeatmaskedslice rmslice,
ajuint level);
AjBool ensRepeatmaskedsliceFetchSequenceSeq(EnsPRepeatmaskedslice rmslice,
EnsERepeatMaskType mtype,
AjPSeq *Psequence);
AjBool ensRepeatmaskedsliceFetchSequenceStr(EnsPRepeatmaskedslice rmslice,
EnsERepeatMaskType mtype,
AjPStr *Psequence);
/*
** End of prototype definitions
*/
AJ_END_DECLS
#endif /* !ENSSLICE_H */
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