/usr/lib/emboss/include/enscoordsystem.h is in emboss-lib 6.6.0+dfsg-6build1.
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**
** Ensembl Coordinate System functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.22 $
** @modified 2009 by Alan Bleasby for incorporation into EMBOSS core
** @modified $Date: 2013/02/17 13:04:02 $ 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 ENSCOORDSYSTEM_H
#define ENSCOORDSYSTEM_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ensdatabaseadaptor.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
struct EnsSCoordsystem;
/* @data EnsPCoordsystemadaptor ***********************************************
**
** Ensembl Coordinate System Adaptor
**
** @alias EnsSCoordsystemadaptor
** @alias EnsOCoordsystemadaptor
**
** @cc Bio::EnsEMBL::DBSQL::BaseAdaptor
** @attr Adaptor [EnsPDatabaseadaptor] Ensembl Database Adaptor
** cc Bio::EnsEMBL::DBSQL::CoordSystemAdaptor
** @attr CacheByIdentifier [AjPTable] Database identifier cache
** @attr CacheByName [AjPTable] Name cache
** @attr CacheByRank [AjPTable] Rank cache
** @attr CacheByDefault [AjPTable] Default Ensembl Coordinate System objects
** @attr MappingPaths [AjPTable] Mapping paths between coordinate systems
** @attr ExternalToInternal [AjPTable]
** AJAX Table of AJAX unsigned integer
** (external Ensembl Sequence Region identifier) key data and
** AJAX unsigned integer
** (internal Ensembl Sequence Region identifier) value data
** @attr InternalToExternal [AjPTable]
** AJAX Table of AJAX unsigned integer
** (internal Ensembl Sequence Region identifier) key data and
** AJAX unsigned integer
** (external Ensembl Sequence Region identifier) value data
** @attr Seqlevel [struct EnsSCoordsystem*]
** Sequence-level Ensembl Coordinate System
** @attr Toplevel [struct EnsSCoordsystem*]
** Top-level Ensembl Coordinate System
** @@
******************************************************************************/
typedef struct EnsSCoordsystemadaptor
{
EnsPDatabaseadaptor Adaptor;
AjPTable CacheByIdentifier;
AjPTable CacheByName;
AjPTable CacheByRank;
AjPTable CacheByDefault;
AjPTable MappingPaths;
AjPTable ExternalToInternal;
AjPTable InternalToExternal;
struct EnsSCoordsystem *Seqlevel;
struct EnsSCoordsystem *Toplevel;
} EnsOCoordsystemadaptor;
#define EnsPCoordsystemadaptor EnsOCoordsystemadaptor*
/* @data EnsPCoordsystem ******************************************************
**
** Ensembl Coordinate System
**
** @alias EnsSCoordsystem
** @alias EnsOCoordsystem
**
** @attr Use [ajuint] Use counter
** @cc Bio::EnsEMBL::Storable
** @attr Identifier [ajuint] Internal SQL database identifier (primary key)
** @attr Adaptor [EnsPCoordsystemadaptor] Ensembl Coordinate System Adaptor
** @cc Bio::EnsEMBL::CoordSystem
** @attr Name [AjPStr] Coordinate System name
** @attr Version [AjPStr] Coordinate System version
** @attr Default [AjBool] Default Coordinate System version of this name
** @attr SequenceLevel [AjBool] Sequence-level attribute
** @attr Toplevel [AjBool] Top-level attribute
** @attr Rank [ajuint] Coordinate System rank
** @@
******************************************************************************/
typedef struct EnsSCoordsystem
{
ajuint Use;
ajuint Identifier;
EnsPCoordsystemadaptor Adaptor;
AjPStr Name;
AjPStr Version;
AjBool Default;
AjBool SequenceLevel;
AjBool Toplevel;
ajuint Rank;
} EnsOCoordsystem;
#define EnsPCoordsystem EnsOCoordsystem*
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
/* Ensembl Coordinate System */
EnsPCoordsystem ensCoordsystemNewCpy(const EnsPCoordsystem cs);
EnsPCoordsystem ensCoordsystemNewIni(EnsPCoordsystemadaptor csa,
ajuint identifier,
AjPStr name,
AjPStr version,
ajuint rank,
AjBool deflt,
AjBool toplvl,
AjBool seqlvl);
EnsPCoordsystem ensCoordsystemNewRef(EnsPCoordsystem cs);
void ensCoordsystemDel(EnsPCoordsystem *Pcs);
EnsPCoordsystemadaptor ensCoordsystemGetAdaptor(const EnsPCoordsystem cs);
AjBool ensCoordsystemGetDefault(const EnsPCoordsystem cs);
ajuint ensCoordsystemGetIdentifier(const EnsPCoordsystem cs);
const AjPStr ensCoordsystemGetName(const EnsPCoordsystem cs);
ajuint ensCoordsystemGetRank(const EnsPCoordsystem cs);
AjBool ensCoordsystemGetSeqlevel(const EnsPCoordsystem cs);
AjBool ensCoordsystemGetToplevel(const EnsPCoordsystem cs);
const AjPStr ensCoordsystemGetVersion(const EnsPCoordsystem cs);
AjBool ensCoordsystemSetAdaptor(EnsPCoordsystem cs,
EnsPCoordsystemadaptor csa);
AjBool ensCoordsystemSetIdentifier(EnsPCoordsystem cs, ajuint identifier);
AjBool ensCoordsystemTrace(const EnsPCoordsystem cs, ajuint level);
size_t ensCoordsystemCalculateMemsize(const EnsPCoordsystem cs);
AjBool ensCoordsystemMatch(const EnsPCoordsystem cs1,
const EnsPCoordsystem cs2);
AjPStr ensCoordsystemGetSpecies(const EnsPCoordsystem cs);
AjBool ensListCoordsystemSortIdentifierAscending(AjPList css);
AjBool ensListCoordsystemSortIdentifierDescending(AjPList css);
AjBool ensListCoordsystemSortRankAscending(AjPList css);
AjBool ensListCoordsystemSortRankDescending(AjPList css);
AjBool ensListCoordsystemTrace(const AjPList css, ajuint level);
/* Ensembl Coordinate System Adaptor */
EnsPCoordsystemadaptor ensRegistryGetCoordsystemadaptor(
EnsPDatabaseadaptor dba);
EnsPCoordsystemadaptor ensCoordsystemadaptorNew(
EnsPDatabaseadaptor dba);
void ensCoordsystemadaptorDel(EnsPCoordsystemadaptor *Pcsa);
EnsPDatabaseadaptor ensCoordsystemadaptorGetDatabaseadaptor(
EnsPCoordsystemadaptor csa);
AjBool ensCoordsystemadaptorFetchAll(
const EnsPCoordsystemadaptor csa,
AjPList css);
AjBool ensCoordsystemadaptorFetchAllbyName(
const EnsPCoordsystemadaptor csa,
const AjPStr name,
AjPList css);
AjBool ensCoordsystemadaptorFetchByIdentifier(
const EnsPCoordsystemadaptor csa,
ajuint identifier,
EnsPCoordsystem *Pcs);
AjBool ensCoordsystemadaptorFetchByName(
const EnsPCoordsystemadaptor csa,
const AjPStr name,
const AjPStr version,
EnsPCoordsystem *Pcs);
AjBool ensCoordsystemadaptorFetchByRank(
const EnsPCoordsystemadaptor csa,
ajuint rank,
EnsPCoordsystem *Pcs);
AjBool ensCoordsystemadaptorFetchSeqlevel(
const EnsPCoordsystemadaptor csa,
EnsPCoordsystem *Pcs);
AjBool ensCoordsystemadaptorFetchToplevel(
const EnsPCoordsystemadaptor csa,
EnsPCoordsystem *Pcs);
const AjPList ensCoordsystemadaptorGetMappingpath(
const EnsPCoordsystemadaptor csa,
EnsPCoordsystem cs1,
EnsPCoordsystem cs2);
ajuint ensCoordsystemadaptorGetSeqregionidentifierExternal(
const EnsPCoordsystemadaptor csa,
ajuint srid);
ajuint ensCoordsystemadaptorGetSeqregionidentifierInternal(
const EnsPCoordsystemadaptor csa,
ajuint srid);
/*
** End of prototype definitions
*/
AJ_END_DECLS
#endif /* !ENSCOORDSYSTEM_H */
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