#ifndef ENSGENE_H
#define ENSGENE_H

/* ==================================================================== */
/* ========================== include files =========================== */
/* ==================================================================== */

#include "ensfeature.h"

AJ_BEGIN_DECLS




/* ==================================================================== */
/* ============================ constants ============================= */
/* ==================================================================== */




/* ==================================================================== */
/* ========================== public data ============================= */
/* ==================================================================== */




/* ==================================================================== */
/* ======================= public functions =========================== */
/* ==================================================================== */

/*
** Prototype definitions
*/

/* Ensembl Gene */

EnsPGene ensGeneNewCpy(const EnsPGene gene);

EnsPGene ensGeneNewIni(EnsPGeneadaptor ga,
                       ajuint identifier,
                       EnsPFeature feature,
                       EnsPDatabaseentry displaydbe,
                       AjPStr description,
                       AjPStr source,
                       AjPStr biotype,
                       EnsEGeneStatus status,
                       AjBool current,
                       ajuint cantrcid,
                       AjPStr canann,
                       AjPStr stableid,
                       ajuint version,
                       AjPStr cdate,
                       AjPStr mdate,
                       AjPList transcripts);

EnsPGene ensGeneNewRef(EnsPGene gene);

void ensGeneDel(EnsPGene* Pgene);

EnsPGeneadaptor ensGeneGetAdaptor(const EnsPGene gene);

AjPStr ensGeneGetBiotype(const EnsPGene gene);

AjPStr ensGeneGetCanonicalannotation(const EnsPGene gene);

ajuint ensGeneGetCanonicaltranscriptidentifier(const EnsPGene gene);

AjBool ensGeneGetCurrent(const EnsPGene gene);

AjPStr ensGeneGetDateCreation(const EnsPGene gene);

AjPStr ensGeneGetDateModification(const EnsPGene gene);

AjPStr ensGeneGetDescription(const EnsPGene gene);

EnsPDatabaseentry ensGeneGetDisplayreference(const EnsPGene gene);

EnsPFeature ensGeneGetFeature(const EnsPGene gene);

ajuint ensGeneGetIdentifier(const EnsPGene gene);

AjPStr ensGeneGetSource(const EnsPGene gene);

AjPStr ensGeneGetStableidentifier(const EnsPGene gene);

EnsEGeneStatus ensGeneGetStatus(const EnsPGene gene);

ajuint ensGeneGetVersion(const EnsPGene gene);

const AjPList ensGeneLoadAttributes(EnsPGene gene);

const AjPList ensGeneLoadDatabaseentries(EnsPGene gene);

const AjPList ensGeneLoadTranscripts(EnsPGene gene);

AjBool ensGeneSetAdaptor(EnsPGene gene, EnsPGeneadaptor ga);

AjBool ensGeneSetBiotype(EnsPGene gene, AjPStr biotype);

AjBool ensGeneSetCanonicalannotation(EnsPGene gene, AjPStr canann);

AjBool ensGeneSetCanonicaltranscriptidentifier(EnsPGene gene, ajuint cantrcid);

AjBool ensGeneSetCurrent(EnsPGene gene, AjBool current);

AjBool ensGeneSetDateCreation(EnsPGene gene, AjPStr cdate);

AjBool ensGeneSetDateModification(EnsPGene gene, AjPStr mdate);

AjBool ensGeneSetDescription(EnsPGene gene, AjPStr description);

AjBool ensGeneSetDisplayreference(EnsPGene gene, EnsPDatabaseentry dbe);

AjBool ensGeneSetFeature(EnsPGene gene, EnsPFeature feature);

AjBool ensGeneSetIdentifier(EnsPGene gene, ajuint identifier);

AjBool ensGeneSetSource(EnsPGene gene, AjPStr source);

AjBool ensGeneSetStableidentifier(EnsPGene gene, AjPStr stableid);

AjBool ensGeneSetStatus(EnsPGene gene, EnsEGeneStatus status);

AjBool ensGeneSetVersion(EnsPGene gene, ajuint version);

AjBool ensGeneAddAttribute(EnsPGene gene, EnsPAttribute attribute);

AjBool ensGeneAddDatabaseentry(EnsPGene gene, EnsPDatabaseentry dbe);

AjBool ensGeneAddTranscript(EnsPGene gene, EnsPTranscript transcript);

AjBool ensGeneTrace(const EnsPGene gene, ajuint level);

size_t ensGeneCalculateMemsize(const EnsPGene gene);

AjBool ensGeneCalculateCoordinates(EnsPGene gene);

AjBool ensGeneFetchAllAttributes(EnsPGene gene,
                                 const AjPStr code,
                                 AjPList attributes);

AjBool ensGeneFetchAllDatabaseentries(EnsPGene gene,
                                      const AjPStr name,
                                      EnsEExternaldatabaseType type,
                                      AjPList dbes);

AjBool ensGeneFetchAllExons(EnsPGene gene, AjPList exons);

AjBool ensGeneFetchCanonicaltranscript(EnsPGene gene,
                                       EnsPTranscript* Ptranscript);

AjBool ensGeneSimilarity(EnsPGene gene1, EnsPGene gene2);

EnsPGene ensGeneTransfer(EnsPGene gene, EnsPSlice slice);

EnsPGene ensGeneTransform(EnsPGene gene,
                          const AjPStr csname,
                          const AjPStr csversion);

EnsEGeneStatus ensGeneStatusFromStr(const AjPStr status);

const char* ensGeneStatusToChar(EnsEGeneStatus status);

AjBool ensListGeneSortStartAscending(AjPList genes);

AjBool ensListGeneSortStartDescending(AjPList genes);

AjBool ensTableGeneClear(AjPTable table);

AjBool ensTableGeneDelete(AjPTable* Ptable);

/* Ensembl Gene Adaptor */

EnsPGeneadaptor ensRegistryGetGeneadaptor(
    EnsPDatabaseadaptor dba);

EnsPGeneadaptor ensGeneadaptorNew(
    EnsPDatabaseadaptor dba);

void ensGeneadaptorDel(EnsPGeneadaptor* Pga);

EnsPDatabaseadaptor ensGeneadaptorGetDatabaseadaptor(const EnsPGeneadaptor ga);

EnsPFeatureadaptor ensGeneadaptorGetFeatureadaptor(const EnsPGeneadaptor ga);

AjBool ensGeneadaptorFetchAll(EnsPGeneadaptor ga,
                              AjPList genes);

AjBool ensGeneadaptorFetchAllbyBiotype(EnsPGeneadaptor ga,
                                       const AjPStr biotype,
                                       AjPList genes);

AjBool ensGeneadaptorFetchAllbySlice(EnsPGeneadaptor ga,
                                     EnsPSlice slice,
                                     const AjPStr anname,
                                     const AjPStr source,
                                     const AjPStr biotype,
                                     AjBool loadtranscripts,
                                     AjPList genes);

AjBool ensGeneadaptorFetchAllbyStableidentifier(EnsPGeneadaptor ga,
                                                const AjPStr stableid,
                                                AjPList genes);

AjBool ensGeneadaptorFetchByDisplaylabel(EnsPGeneadaptor ga,
                                         const AjPStr label,
                                         EnsPGene* Pgene);

AjBool ensGeneadaptorFetchByIdentifier(EnsPGeneadaptor ga,
                                       ajuint identifier,
                                       EnsPGene* Pgene);

AjBool ensGeneadaptorFetchByStableidentifier(EnsPGeneadaptor ga,
                                             const AjPStr stableid,
                                             ajuint version,
                                             EnsPGene* Pgene);

AjBool ensGeneadaptorRetrieveAllIdentifiers(EnsPGeneadaptor ga,
                                            AjPList identifiers);

AjBool ensGeneadaptorRetrieveAllStableidentifiers(EnsPGeneadaptor ga,
                                                  AjPList identifiers);

/*
** End of prototype definitions
*/




AJ_END_DECLS

#endif /* !ENSGENE_H */