#ifndef ENSTRANSLATION_H
#define ENSTRANSLATION_H

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

#include "ensdata.h"
#include "ensprotein.h"

AJ_BEGIN_DECLS




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




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




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

/*
** Prototype definitions
*/

void ensTranslationInit(void);

void ensTranslationExit(void);

const AjPTrn ensTranslationCacheGet(ajint codontable);

/* Ensembl Translation */

EnsPTranslation ensTranslationNewCpy(const EnsPTranslation translation);

EnsPTranslation ensTranslationNewIni(EnsPTranslationadaptor tla,
                                     ajuint identifier,
                                     EnsPExon startexon,
                                     EnsPExon endexon,
                                     ajuint start,
                                     ajuint end,
                                     AjPStr sequence,
                                     AjPStr stableid,
                                     ajuint version,
                                     AjPStr cdate,
                                     AjPStr mdate);

EnsPTranslation ensTranslationNewRef(EnsPTranslation translation);

void ensTranslationDel(EnsPTranslation* Ptranslation);

EnsPTranslationadaptor ensTranslationGetAdaptor(
    const EnsPTranslation translation);

AjPStr ensTranslationGetDateCreation(const EnsPTranslation translation);

AjPStr ensTranslationGetDateModification(const EnsPTranslation translation);

ajuint ensTranslationGetEnd(const EnsPTranslation translation);

EnsPExon ensTranslationGetEndexon(const EnsPTranslation translation);

ajuint ensTranslationGetIdentifier(const EnsPTranslation translation);

AjPStr ensTranslationGetStableidentifier(const EnsPTranslation translation);

ajuint ensTranslationGetStart(const EnsPTranslation translation);

EnsPExon ensTranslationGetStartexon(const EnsPTranslation translation);

ajuint ensTranslationGetVersion(const EnsPTranslation translation);

const AjPList ensTranslationLoadAttributes(EnsPTranslation translation);

const AjPList ensTranslationLoadDatabaseentries(EnsPTranslation translation);

const AjPList ensTranslationLoadProteinfeatures(EnsPTranslation translation);

AjBool ensTranslationSetAdaptor(EnsPTranslation translation,
                                EnsPTranslationadaptor tla);

AjBool ensTranslationSetIdentifier(EnsPTranslation translation,
                                   ajuint identifier);

AjBool ensTranslationSetStartexon(EnsPTranslation translation,
                                  EnsPExon exon);

AjBool ensTranslationSetEndexon(EnsPTranslation translation,
                                EnsPExon exon);

AjBool ensTranslationSetStart(EnsPTranslation translation,
                              ajuint start);

AjBool ensTranslationSetEnd(EnsPTranslation translation,
                            ajuint end);

AjBool ensTranslationSetStableidentifier(EnsPTranslation translation,
                                         AjPStr stableid);

AjBool ensTranslationSetVersion(EnsPTranslation translation,
                                ajuint version);

AjBool ensTranslationSetDateCreation(EnsPTranslation translation,
                                     AjPStr cdate);

AjBool ensTranslationSetDateModification(EnsPTranslation translation,
                                         AjPStr mdate);

AjBool ensTranslationAddAttribute(EnsPTranslation translation,
                                  EnsPAttribute attribute);

AjBool ensTranslationAddDatabaseentry(EnsPTranslation translation,
                                      EnsPDatabaseentry dbe);

AjBool ensTranslationAddProteinfeature(EnsPTranslation translation,
                                       EnsPProteinfeature pf);

size_t ensTranslationCalculateMemsize(const EnsPTranslation translation);

ajint ensTranslationCalculateSliceEnd(EnsPTranslation translation);

ajint ensTranslationCalculateSliceStart(EnsPTranslation translation);

ajuint ensTranslationCalculateTranscriptEnd(EnsPTranslation translation);

ajuint ensTranslationCalculateTranscriptStart(EnsPTranslation translation);

AjBool ensTranslationFetchAllAttributes( EnsPTranslation translation,
                                         const AjPStr code,
                                         AjPList attributes);

AjBool ensTranslationFetchAllDatabaseentries(EnsPTranslation translation,
                                             const AjPStr name,
                                             EnsEExternaldatabaseType type,
                                             AjPList dbes);

AjBool ensTranslationFetchAllDomains(EnsPTranslation translation,
                                     AjPList pfs);

AjBool ensTranslationFetchAllProteinfeatures(EnsPTranslation translation,
                                             const AjPStr name,
                                             AjPList pfs);

AjBool ensTranslationFetchAllSequenceedits(EnsPTranslation translation,
                                           AjPList ses);

AjBool ensTranslationFetchDisplayidentifier(const EnsPTranslation translation,
                                            AjPStr* Pidentifier);

AjBool ensTranslationTrace(const EnsPTranslation translation, ajuint level);

AjBool ensTranslationFetchSequenceSeq(EnsPTranslation translation,
                                      AjPSeq* Psequence);

AjBool ensTranslationFetchSequenceStr(EnsPTranslation translation,
                                      AjPStr* Psequence);

/* Ensembl Translation Adaptor */

EnsPTranslationadaptor ensRegistryGetTranslationadaptor(
    EnsPDatabaseadaptor dba);

EnsPTranslationadaptor ensTranslationadaptorNew(
    EnsPDatabaseadaptor dba);

void ensTranslationadaptorDel(EnsPTranslationadaptor* Ptla);

EnsPDatabaseadaptor ensTranslationadaptorGetDatabaseadaptor(
    EnsPTranslationadaptor tla);

AjBool ensTranslationadaptorFetchAllbyExternalname(
    EnsPTranslationadaptor tla,
    const AjPStr name,
    const AjPStr dbname,
    AjPList translations);

AjBool ensTranslationadaptorFetchAllbyTranscript(EnsPTranslationadaptor tla,
                                                 EnsPTranscript transcript);

AjBool ensTranslationadaptorFetchByIdentifier(EnsPTranslationadaptor tla,
                                              ajuint identifier,
                                              EnsPTranslation* Ptranslation);

AjBool ensTranslationadaptorFetchByStableidentifier(
    EnsPTranslationadaptor tla,
    const AjPStr stableid,
    ajuint version,
    EnsPTranslation* Ptranslation);

AjBool ensTranslationadaptorFetchByTranscript(EnsPTranslationadaptor tla,
                                              EnsPTranscript transcript);

AjBool ensTranslationadaptorFetchAllbyTranscriptsList(
    EnsPTranslationadaptor tla,
    AjPList transcripts);

AjBool ensTranslationadaptorFetchAllbyTranscriptsTable(
    EnsPTranslationadaptor tla,
    AjPTable transcripts);

AjBool ensTranslationadaptorRetrieveAllIdentifiers(
    EnsPTranslationadaptor tla,
    AjPList identifiers);

AjBool ensTranslationadaptorRetrieveAllStableidentifiers(
    EnsPTranslationadaptor tla,
    AjPList identifiers);

/*
** End of prototype definitions
*/




AJ_END_DECLS

#endif /* !ENSTRANSLATION_H */