#ifndef ENSGVVARIATION_H
#define ENSGVVARIATION_H

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

#include "ensgvdata.h"

AJ_BEGIN_DECLS




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




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




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

/*
** Prototype definitions
*/

/* Ensembl Genetic Variation Variation */

EnsPGvvariation ensGvvariationNewCpy(const EnsPGvvariation gvv);

EnsPGvvariation ensGvvariationNewIni(EnsPGvvariationadaptor gvva,
                                     ajuint identifier,
                                     EnsPGvattribute classgva,
                                     EnsPGvsource gvsource,
                                     AjPStr name,
                                     AjPStr ancestralallele,
                                     AjPList gvalleles,
                                     AjPList gvsynonyms,
                                     AjPStr validationstates,
                                     AjPStr moltype,
                                     AjPStr flankfive,
                                     AjPStr flankthree,
                                     AjBool flankexists,
                                     AjBool somatic);

EnsPGvvariation ensGvvariationNewRef(EnsPGvvariation gvv);

void ensGvvariationDel(EnsPGvvariation* Pgvv);

EnsPGvvariationadaptor ensGvvariationGetAdaptor(const EnsPGvvariation gvv);

AjPStr ensGvvariationGetAncestralallele(const EnsPGvvariation gvv);

EnsPGvattribute ensGvvariationGetClass(const EnsPGvvariation gvv);

AjBool ensGvvariationGetFlankExists(const EnsPGvvariation gvv);

const AjPList ensGvvariationGetGvalleles(const EnsPGvvariation gvv);

EnsPGvsource ensGvvariationGetGvsource(const EnsPGvvariation gvv);

const AjPList ensGvvariationGetGvsynonyms(const EnsPGvvariation gvv);

ajuint ensGvvariationGetIdentifier(const EnsPGvvariation gvv);

AjPStr ensGvvariationGetMoleculetype(const EnsPGvvariation gvv);

AjPStr ensGvvariationGetName(const EnsPGvvariation gvv);

AjBool ensGvvariationGetSomatic(const EnsPGvvariation gvv);

ajuint ensGvvariationGetValidations(const EnsPGvvariation gvv);

const AjPList ensGvvariationLoadAllFaileddescriptions(EnsPGvvariation gvv);

AjPStr ensGvvariationLoadFlankFive(EnsPGvvariation gvv);

AjPStr ensGvvariationLoadFlankThree(EnsPGvvariation gvv);

AjBool ensGvvariationSetAdaptor(EnsPGvvariation gvv,
                                EnsPGvvariationadaptor gvva);

AjBool ensGvvariationSetAncestralallele(EnsPGvvariation gvv,
                                        AjPStr ancestralallele);

AjBool ensGvvariationSetClass(EnsPGvvariation gvv,
                              EnsPGvattribute classgva);

AjBool ensGvvariationSetFlankExists(EnsPGvvariation gvv,
                                    AjBool flankexists);

AjBool ensGvvariationSetFlankFive(EnsPGvvariation gvv,
                                  AjPStr flankfive);

AjBool ensGvvariationSetFlankThree(EnsPGvvariation gvv,
                                   AjPStr flankthree);

AjBool ensGvvariationSetGvsource(EnsPGvvariation gvv,
                                 EnsPGvsource gvs);

AjBool ensGvvariationSetIdentifier(EnsPGvvariation gvv,
                                   ajuint identifier);

AjBool ensGvvariationSetMoleculetype(EnsPGvvariation gvv,
                                     AjPStr moltype);

AjBool ensGvvariationSetName(EnsPGvvariation gvv,
                             AjPStr name);

AjBool ensGvvariationSetSomatic(EnsPGvvariation gvv,
                                AjBool somatic);

AjBool ensGvvariationTrace(const EnsPGvvariation gvv, ajuint level);

size_t ensGvvariationCalculateMemsize(const EnsPGvvariation gvv);

AjBool ensGvvariationAddFaileddescription(EnsPGvvariation gvv,
                                          AjPStr description);

AjBool ensGvvariationAddGvallele(EnsPGvvariation gvv,
                                 EnsPGvallele gva);

AjBool ensGvvariationAddGvsynonym(EnsPGvvariation gvv,
                                  EnsPGvsynonym gvs);

AjBool ensGvvariationAddValidation(EnsPGvvariation gvv,
                                   EnsEGvvariationValidation gvvv);

AjBool ensGvvariationFetchAllGenes(EnsPGvvariation gvv,
                                   ajint flank,
                                   AjPList genes);

AjBool ensGvvariationFetchAllGvsources(const EnsPGvvariation gvv,
                                       AjPList gvss);

AjBool ensGvvariationFetchAllGvsynonyms(const EnsPGvvariation gvv,
                                        const AjPStr gvsourcename,
                                        AjPList gvss);

AjBool ensGvvariationFetchAllGvvariationfeatures(EnsPGvvariation gvv,
                                                 AjPList gvvfs);

AjBool ensGvvariationHasFailedgvalleles(EnsPGvvariation gvv, AjBool* Presult);

AjBool ensGvvariationIsFailed(EnsPGvvariation gvv, AjBool* Presult);

EnsEGvvariationClass ensGvvariationClassFromStr(
    const AjPStr class);

const char* ensGvvariationClassToChar(
    EnsEGvvariationClass gvvc);

EnsEGvvariationValidation ensGvvariationValidationFromStr(
    const AjPStr validation);

const char* ensGvvariationValidationToChar(
    EnsEGvvariationValidation gvvv);

ajuint ensGvvariationValidationsFromSet(const AjPStr gvvvset);

AjBool ensGvvariationValidationsToSet(ajuint gvvvbf, AjPStr* Pgvvvset);

AjBool ensTableGvvariationClear(AjPTable table);

AjBool ensTableGvvariationDelete(AjPTable* Ptable);

/* Ensembl Genetic Variation Variation Adaptor */

EnsPGvvariationadaptor ensRegistryGetGvvariationadaptor(
    EnsPDatabaseadaptor dba);

AjBool ensGvvariationadaptorFetchAllbyGvpopulation(
    EnsPGvvariationadaptor gvva,
    const EnsPGvpopulation gvp,
    AjPList gvvs);

AjBool ensGvvariationadaptorFetchAllbyGvpopulationfrequency(
    EnsPGvvariationadaptor gvva,
    const EnsPGvpopulation gvp,
    float frequency,
    AjPList gvvs);

AjBool ensGvvariationadaptorFetchAllbyGvsourceType(
    EnsPGvvariationadaptor gvva,
    EnsEGvsourceType gvst,
    AjBool primary,
    AjPList gvvs);

AjBool ensGvvariationadaptorFetchAllbyGvvariationset(
    EnsPGvvariationadaptor gvva,
    EnsPGvvariationset gvvset,
    AjPList gvvs);

AjBool ensGvvariationadaptorFetchAllbyIdentifiers(
    EnsPGvvariationadaptor gvva,
    AjPTable gvvs);

AjBool ensGvvariationadaptorFetchAllbyNames(
    EnsPGvvariationadaptor gvva,
    AjPTable gvvs);

AjBool ensGvvariationadaptorFetchAllbySource(
    EnsPGvvariationadaptor gvva,
    const AjPStr source,
    AjBool primary,
    AjPList gvvs);

AjBool ensGvvariationadaptorFetchByIdentifier(
    EnsPGvvariationadaptor gvva,
    ajuint identifier,
    EnsPGvvariation* Pgvv);

AjBool ensGvvariationadaptorFetchByName(
    EnsPGvvariationadaptor gvva,
    const AjPStr name,
    const AjPStr source,
    EnsPGvvariation* Pgvv);

AjBool ensGvvariationadaptorFetchBySubidentifier(
    EnsPGvvariationadaptor gvva,
    const AjPStr name,
    EnsPGvvariation* Pgvv);

AjBool ensGvvariationadaptorRetrieveAllFaileddescriptions(
    EnsPGvvariationadaptor gvva,
    ajuint identifier,
    AjPList fvs);

AjBool ensGvvariationadaptorRetrieveFlank(
    EnsPGvvariationadaptor gvva,
    ajuint identifier,
    AjPStr* Pfiveseq,
    AjPStr* Pthreeseq);

/* Ensembl Genetic Variation Variation Feature */

EnsPGvvariationfeature ensGvvariationfeatureNewCpy(
    const EnsPGvvariationfeature gvvf);

EnsPGvvariationfeature ensGvvariationfeatureNewIdentifier(
    EnsPGvvariationfeatureadaptor gvvfa,
    ajuint identifier,
    EnsPFeature feature,
    EnsPGvsource gvsource,
    EnsEGvvariationClass gvvc,
    ajuint gvvidentifier,
    AjPStr allele,
    AjPStr name,
    AjPStr validation,
    AjPStr consequence,
    ajuint mapweight);

EnsPGvvariationfeature ensGvvariationfeatureNewIni(
    EnsPGvvariationfeatureadaptor gvvfa,
    ajuint identifier,
    EnsPFeature feature,
    EnsPGvsource gvsource,
    EnsEGvvariationClass gvvc,
    EnsPGvvariation gvv,
    AjPStr allele,
    AjPStr name,
    AjPStr validation,
    AjPStr consequence,
    ajuint mapweight);

EnsPGvvariationfeature ensGvvariationfeatureNewRef(
    EnsPGvvariationfeature gvvf);

void ensGvvariationfeatureDel(EnsPGvvariationfeature* Pgvvf);

EnsPGvvariationfeatureadaptor ensGvvariationfeatureGetAdaptor(
    const EnsPGvvariationfeature gvvf);

AjPStr ensGvvariationfeatureGetAllele(
    const EnsPGvvariationfeature gvvf);

AjPStr ensGvvariationfeatureGetConsequencetype(
    const EnsPGvvariationfeature gvvf);

EnsPFeature ensGvvariationfeatureGetFeature(
    const EnsPGvvariationfeature gvvf);

EnsPGvsource ensGvvariationfeatureGetGvsource(
    const EnsPGvvariationfeature gvvf);

EnsEGvvariationClass ensGvvariationfeatureGetGvvariationclass(
    const EnsPGvvariationfeature gvvf);

ajuint ensGvvariationfeatureGetIdentifier(
    const EnsPGvvariationfeature gvvf);

ajuint ensGvvariationfeatureGetMapweight(
    const EnsPGvvariationfeature gvvf);

AjPStr ensGvvariationfeatureGetName(
    const EnsPGvvariationfeature gvvf);

AjPStr ensGvvariationfeatureGetValidationcode(
    const EnsPGvvariationfeature gvvf);

EnsPGvvariation ensGvvariationfeatureLoadGvvariation(
    EnsPGvvariationfeature gvvf);

AjBool ensGvvariationfeatureSetAdaptor(EnsPGvvariationfeature gvvf,
                                       EnsPGvvariationfeatureadaptor gvvfa);

AjBool ensGvvariationfeatureSetAllele(EnsPGvvariationfeature gvvf,
                                      AjPStr allele);

AjBool ensGvvariationfeatureSetConsequencetype(EnsPGvvariationfeature gvvf,
                                               AjPStr consequencetype);

AjBool ensGvvariationfeatureSetFeature(EnsPGvvariationfeature gvvf,
                                       EnsPFeature feature);

AjBool ensGvvariationfeatureSetGvsource(EnsPGvvariationfeature gvvf,
                                        EnsPGvsource gvsource);

AjBool ensGvvariationfeatureSetGvvariation(EnsPGvvariationfeature gvvf,
                                           EnsPGvvariation gvv);

AjBool ensGvvariationfeatureSetGvvariationclass(EnsPGvvariationfeature gvvf,
                                                EnsEGvvariationClass gvvc);

AjBool ensGvvariationfeatureSetIdentifier(EnsPGvvariationfeature gvvf,
                                          ajuint identifier);

AjBool ensGvvariationfeatureSetMapweight(EnsPGvvariationfeature gvvf,
                                         ajuint mapweight);

AjBool ensGvvariationfeatureSetName(EnsPGvvariationfeature gvvf,
                                    AjPStr name);

AjBool ensGvvariationfeatureSetValidationcode(EnsPGvvariationfeature gvvf,
                                              AjPStr validationcode);

AjBool ensGvvariationfeatureTrace(const EnsPGvvariationfeature gvvf,
                                  ajuint level);

ajuint ensGvvariationfeatureCalculateLength(
    const EnsPGvvariationfeature gvvf);

size_t ensGvvariationfeatureCalculateMemsize(
    const EnsPGvvariationfeature gvvf);

AjBool ensGvvariationfeatureGetSomatic(
    const EnsPGvvariationfeature gvvf);

AjPStr ensGvvariationfeatureGetSourcename(
    const EnsPGvvariationfeature gvvf);

AjBool ensGvvariationfeatureIsReference(EnsPGvvariationfeature gvvf,
                                        AjBool* Presult);

AjBool ensListGvvariationfeatureSortStartAscending(AjPList gvvfs);

AjBool ensListGvvariationfeatureSortStartDescending(AjPList gvvfs);

/* Ensembl Genetic Variation Feature Adaptor */

EnsPGvvariationfeatureadaptor ensRegistryGetGvvariationfeatureadaptor(
    EnsPDatabaseadaptor dba);

EnsPGvvariationfeatureadaptor ensGvvariationfeatureadaptorNew(
    EnsPDatabaseadaptor dba);

void ensGvvariationfeatureadaptorDel(EnsPGvvariationfeatureadaptor* Pgvvfa);

EnsPDatabaseadaptor ensGvvariationfeatureadaptorGetDatabaseadaptor(
    const EnsPGvvariationfeatureadaptor gvvfa);

EnsPFeatureadaptor ensGvvariationfeatureadaptorGetFeatureadaptor(
    const EnsPGvvariationfeatureadaptor gvvfa);

EnsPGvdatabaseadaptor ensGvvariationfeatureadaptorGetGvdatabaseadaptor(
    const EnsPGvvariationfeatureadaptor gvvfa);

AjBool ensGvvariationfeatureadaptorFetchAllbyFrequency(
    EnsPGvvariationfeatureadaptor gvvfa,
    const EnsPGvpopulation gvp,
    float frequency,
    EnsPSlice slice,
    AjPList gvvfs);

AjBool ensGvvariationfeatureadaptorFetchAllbyGvpopulation(
    EnsPGvvariationfeatureadaptor gvvfa,
    const EnsPGvpopulation gvp,
    EnsPSlice slice,
    AjPList gvvfs);

AjBool ensGvvariationfeatureadaptorFetchAllbyGvvariation(
    EnsPGvvariationfeatureadaptor gvvfa,
    const EnsPGvvariation gvv,
    AjPList gvvfs);

AjBool ensGvvariationfeatureadaptorFetchAllbySliceAnnotated(
    EnsPGvvariationfeatureadaptor gvvfa,
    const AjPStr vsource,
    const AjPStr psource,
    const AjPStr annotation,
    AjBool somatic,
    EnsPSlice slice,
    AjPList gvvfs);

AjBool ensGvvariationfeatureadaptorFetchAllbySliceConstraint(
    EnsPGvvariationfeatureadaptor gvvfa,
    EnsPSlice slice,
    const AjPStr constraint,
    AjBool somatic,
    AjPList gvvfs);

AjBool ensGvvariationfeatureadaptorFetchAllbySliceGenotyped(
    EnsPGvvariationfeatureadaptor gvvfa,
    EnsPSlice slice,
    AjPList gvvfs);

AjBool ensGvvariationfeatureadaptorFetchByIdentifier(
    EnsPGvvariationfeatureadaptor gvvfa,
    ajuint identifier,
    EnsPGvvariationfeature* Pgvvf);

AjBool ensGvvariationfeatureadaptorRetrieveAllIdentifiers(
    EnsPGvvariationfeatureadaptor gvvfa,
    AjPList identifiers);

/* Ensembl Genetic Variation Variation Set */

EnsPGvvariationset ensGvvariationsetNewCpy(const EnsPGvvariationset gvvs);

EnsPGvvariationset ensGvvariationsetNewIni(EnsPGvvariationsetadaptor gvvsa,
                                           ajuint identifier,
                                           AjPStr name,
                                           AjPStr description);

EnsPGvvariationset ensGvvariationsetNewRef(EnsPGvvariationset gvvs);

void ensGvvariationsetDel(EnsPGvvariationset* Pgvvs);

EnsPGvvariationsetadaptor ensGvvariationsetGetAdaptor(
    const EnsPGvvariationset gvvs);

AjPStr ensGvvariationsetGetDescription(
    const EnsPGvvariationset gvvs);

ajuint ensGvvariationsetGetIdentifier(
    const EnsPGvvariationset gvvs);

AjPStr ensGvvariationsetGetName(
    const EnsPGvvariationset gvvs);

AjBool ensGvvariationsetSetAdaptor(EnsPGvvariationset gvvs,
                                   EnsPGvvariationsetadaptor gvvsa);

AjBool ensGvvariationsetSetDescription(EnsPGvvariationset gvvs,
                                       AjPStr description);

AjBool ensGvvariationsetSetIdentifier(EnsPGvvariationset gvvs,
                                      ajuint identifier);

AjBool ensGvvariationsetSetName(EnsPGvvariationset gvvs,
                                AjPStr name);

AjBool ensGvvariationsetTrace(const EnsPGvvariationset gvvs,
                              ajuint level);

size_t ensGvvariationsetCalculateMemsize(const EnsPGvvariationset gvvs);

AjBool ensGvvariationsetFetchAllGvvariations(
    EnsPGvvariationset gvvs,
    AjPList gvvss);

AjBool ensGvvariationsetFetchAllSub(EnsPGvvariationset gvvs,
                                    AjBool immediate,
                                    AjPList gvvss);

AjBool ensGvvariationsetFetchAllSuper(EnsPGvvariationset gvvs,
                                      AjBool immediate,
                                      AjPList gvvss);

/* Ensembl Genetic Variation Variation Set Adaptor */

EnsPGvvariationsetadaptor ensRegistryGetGvvariationsetadaptor(
    EnsPDatabaseadaptor dba);

EnsPGvvariationsetadaptor ensGvvariationsetadaptorNew(
    EnsPDatabaseadaptor dba);

void ensGvvariationsetadaptorDel(EnsPGvvariationsetadaptor* Pgvvsa);

AjBool ensGvvariationsetadaptorFetchAllToplevel(
    EnsPGvvariationsetadaptor gvvsa,
    AjPList gvvss);

AjBool ensGvvariationsetadaptorFetchAllbyGvvariation(
    EnsPGvvariationsetadaptor gvvsa,
    const EnsPGvvariation gvv,
    AjPList gvvss);

AjBool ensGvvariationsetadaptorFetchAllbySub(
    EnsPGvvariationsetadaptor gvvsa,
    const EnsPGvvariationset gvvs,
    AjBool immediate,
    AjPList gvvss);

AjBool ensGvvariationsetadaptorFetchAllbySuper(
    EnsPGvvariationsetadaptor gvvsa,
    const EnsPGvvariationset gvvs,
    AjBool immediate,
    AjPList gvvss);

AjBool ensGvvariationsetadaptorFetchByIdentifier(
    EnsPGvvariationsetadaptor gvvsa,
    ajuint identifier,
    EnsPGvvariationset* Pgvvs);

AjBool ensGvvariationsetadaptorFetchByName(
    EnsPGvvariationsetadaptor gvvsa,
    const AjPStr name,
    EnsPGvvariationset* Pgvvs);

/*
** End of prototype definitions
*/




AJ_END_DECLS

#endif /* !ENSGVVARIATION_H */