#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);

/* Ensembl Sequence Region Adaptor */

EnsPSeqregionadaptor ensRegistryGetSeqregionadaptor(
    EnsPDatabaseadaptor dba);

EnsPSeqregionadaptor ensSeqregionadaptorNew(
    EnsPDatabaseadaptor dba);

void ensSeqregionadaptorDel(EnsPSeqregionadaptor* Psra);

EnsPDatabaseadaptor ensSeqregionadaptorGetDatabaseadaptor(
    const 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(
    const 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 */