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/* @include ensseqregion ******************************************************
**
** Ensembl Sequence Region functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.23 $
** @modified 2009 by Alan Bleasby for incorporation into EMBOSS core
** @modified $Date: 2012/08/05 11:27:31 $ 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 ENSSEQREGION_H
#define ENSSEQREGION_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "enscoordsystem.h"
#include "ensdata.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
/* Ensembl Sequence Region */
EnsPSeqregion ensSeqregionNewCpy(EnsPSeqregion sr);
EnsPSeqregion ensSeqregionNewIni(EnsPSeqregionadaptor sra,
ajuint identifier,
EnsPCoordsystem cs,
AjPStr name,
ajint length);
EnsPSeqregion ensSeqregionNewRef(EnsPSeqregion sr);
void ensSeqregionDel(EnsPSeqregion *Psr);
EnsPSeqregionadaptor ensSeqregionGetAdaptor(const EnsPSeqregion sr);
EnsPCoordsystem ensSeqregionGetCoordsystem(const EnsPSeqregion sr);
ajuint ensSeqregionGetIdentifier(const EnsPSeqregion sr);
ajint ensSeqregionGetLength(const EnsPSeqregion sr);
AjPStr ensSeqregionGetName(const EnsPSeqregion sr);
const AjPList ensSeqregionLoadAttributes(EnsPSeqregion sr);
const AjPList ensSeqregionLoadSeqregionsynonyms(EnsPSeqregion sr);
AjBool ensSeqregionSetAdaptor(EnsPSeqregion sr, EnsPSeqregionadaptor sra);
AjBool ensSeqregionSetCoordsystem(EnsPSeqregion sr, EnsPCoordsystem cs);
AjBool ensSeqregionSetIdentifier(EnsPSeqregion sr, ajuint identifier);
AjBool ensSeqregionSetLength(EnsPSeqregion sr, ajint length);
AjBool ensSeqregionSetName(EnsPSeqregion sr, AjPStr name);
AjBool ensSeqregionAddAttribute(EnsPSeqregion sr, EnsPAttribute attribute);
AjBool ensSeqregionAddSeqregionsynonym(EnsPSeqregion sr,
EnsPSeqregionsynonym srs);
AjBool ensSeqregionTrace(const EnsPSeqregion sr, ajuint level);
size_t ensSeqregionCalculateMemsize(const EnsPSeqregion sr);
AjBool ensSeqregionMatch(const EnsPSeqregion sr1, const EnsPSeqregion sr2);
AjBool ensSeqregionFetchAllAttributes(EnsPSeqregion sr,
const AjPStr code,
AjPList attributes);
AjBool ensSeqregionIsLocusreferencegenomic(EnsPSeqregion sr, AjBool *Presult);
AjBool ensSeqregionIsNonreference(EnsPSeqregion sr, AjBool *Presult);
AjBool ensSeqregionIsToplevel(EnsPSeqregion sr, AjBool *Presult);
AjBool ensListSeqregionSortIdentifierAscending(AjPList srs);
AjBool ensListSeqregionSortIdentifierDescending(AjPList srs);
AjBool ensListSeqregionSortNameAscending(AjPList srs);
AjBool ensListSeqregionSortNameDescending(AjPList srs);
/* Ensembl Sequence Region Adaptor */
EnsPSeqregionadaptor ensRegistryGetSeqregionadaptor(
EnsPDatabaseadaptor dba);
EnsPSeqregionadaptor ensSeqregionadaptorNew(
EnsPDatabaseadaptor dba);
void ensSeqregionadaptorDel(EnsPSeqregionadaptor *Psra);
EnsPDatabaseadaptor ensSeqregionadaptorGetDatabaseadaptor(
EnsPSeqregionadaptor sra);
const AjPList ensSeqregionadaptorLoadLocusreferencegenomic(
EnsPSeqregionadaptor sra);
const AjPList ensSeqregionadaptorLoadNonreferences(
EnsPSeqregionadaptor sra);
AjBool ensSeqregionadaptorCacheInsert(EnsPSeqregionadaptor sra,
EnsPSeqregion *Psr);
AjBool ensSeqregionadaptorCacheRemove(EnsPSeqregionadaptor sra,
const EnsPSeqregion sr);
AjBool ensSeqregionadaptorFetchAllbyAttributecodevalue(
EnsPSeqregionadaptor sra,
const AjPStr code,
const AjPStr value,
AjPList srs);
AjBool ensSeqregionadaptorFetchAllbyCoordsystem(EnsPSeqregionadaptor sra,
const EnsPCoordsystem cs,
AjPList srs);
AjBool ensSeqregionadaptorFetchByIdentifier(EnsPSeqregionadaptor sra,
ajuint identifier,
EnsPSeqregion *Psr);
AjBool ensSeqregionadaptorFetchByName(EnsPSeqregionadaptor sra,
const EnsPCoordsystem cs,
const AjPStr name,
EnsPSeqregion *Psr);
AjBool ensSeqregionadaptorFetchByNamefuzzy(EnsPSeqregionadaptor sra,
const EnsPCoordsystem cs,
const AjPStr name,
EnsPSeqregion *Psr);
AjBool ensSeqregionadaptorFetchBySynonym(EnsPSeqregionadaptor sra,
const AjPStr synonym,
EnsPSeqregion *Psr);
AjBool ensSeqregionadaptorIsLocusreferencegenomic(EnsPSeqregionadaptor sra,
const EnsPSeqregion sr,
AjBool *Presult);
AjBool ensSeqregionadaptorIsNonreference(EnsPSeqregionadaptor sra,
const EnsPSeqregion sr,
AjBool *Presult);
/* Ensembl Sequence Region Synonym */
EnsPSeqregionsynonym ensSeqregionsynonymNewCpy(EnsPSeqregionsynonym srs);
EnsPSeqregionsynonym ensSeqregionsynonymNewIni(
EnsPSeqregionsynonymadaptor srsa,
ajuint identifier,
EnsPExternaldatabase edb,
AjPStr name,
ajuint srid);
EnsPSeqregionsynonym ensSeqregionsynonymNewRef(EnsPSeqregionsynonym srs);
void ensSeqregionsynonymDel(EnsPSeqregionsynonym *Psrs);
EnsPSeqregionsynonymadaptor ensSeqregionsynonymGetAdaptor(
const EnsPSeqregionsynonym srs);
EnsPExternaldatabase ensSeqregionsynonymGetExternaldatabase(
const EnsPSeqregionsynonym srs);
ajuint ensSeqregionsynonymGetIdentifier(
const EnsPSeqregionsynonym srs);
AjPStr ensSeqregionsynonymGetName(
const EnsPSeqregionsynonym srs);
ajuint ensSeqregionsynonymGetSeqregionidentifier(
const EnsPSeqregionsynonym srs);
AjBool ensSeqregionsynonymSetAdaptor(EnsPSeqregionsynonym srs,
EnsPSeqregionsynonymadaptor srsa);
AjBool ensSeqregionsynonymSetExternaldatabase(EnsPSeqregionsynonym srs,
EnsPExternaldatabase edb);
AjBool ensSeqregionsynonymSetIdentifier(EnsPSeqregionsynonym srs,
ajuint identifier);
AjBool ensSeqregionsynonymSetName(EnsPSeqregionsynonym srs,
AjPStr name);
AjBool ensSeqregionsynonymSetSeqregionidentifier(EnsPSeqregionsynonym srs,
ajuint srid);
AjBool ensSeqregionsynonymTrace(const EnsPSeqregionsynonym srs, ajuint level);
size_t ensSeqregionsynonymCalculateMemsize(const EnsPSeqregionsynonym srs);
/* Ensembl Sequence Region Synonym Adaptor */
EnsPSeqregionsynonymadaptor ensRegistryGetSeqregionsynonymadaptor(
EnsPDatabaseadaptor dba);
EnsPSeqregionsynonymadaptor ensSeqregionsynonymadaptorNew(
EnsPDatabaseadaptor dba);
void ensSeqregionsynonymadaptorDel(EnsPSeqregionsynonymadaptor *Psrsa);
EnsPBaseadaptor ensSeqregionsynonymadaptorGetBaseadaptor(
EnsPSeqregionsynonymadaptor srsa);
EnsPDatabaseadaptor ensSeqregionsynonymadaptorGetDatabaseadaptor(
EnsPSeqregionsynonymadaptor srsa);
AjBool ensSeqregionsynonymadaptorFetchAllbySeqregion(
EnsPSeqregionsynonymadaptor srsa,
const EnsPSeqregion sr,
AjPList srss);
AjBool ensSeqregionsynonymadaptorFetchByIdentifier(
EnsPSeqregionsynonymadaptor srsa,
ajuint identifier,
EnsPSeqregionsynonym *Psrs);
AjBool ensSeqregionsynonymadaptorFetchBySynonym(
EnsPSeqregionsynonymadaptor srsa,
const AjPStr synonym,
EnsPSeqregionsynonym *Psrs);
/*
** End of prototype definitions
*/
AJ_END_DECLS
#endif /* !ENSSEQREGION_H */
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