#ifndef ENSPREDICTION_H
#define ENSPREDICTION_H

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

#include "ensfeature.h"

AJ_BEGIN_DECLS




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

/* @const EnsPPredictionexonadaptor *******************************************
**
** Ensembl Prediction Exon Adaptor
**
** Bio::EnsEMBL::DBSQL::PredictionExonAdaptor
**
******************************************************************************/

#define EnsPPredictionexonadaptor EnsPFeatureadaptor




/* @const EnsPPredictiontranscriptadaptor *************************************
**
** Ensembl Prediction Transcript Adaptor
**
** Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor
**
******************************************************************************/

#define EnsPPredictiontranscriptadaptor EnsPFeatureadaptor




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

/* @data EnsPPredictionexon ***************************************************
**
** Ensembl Prediction Exon.
**
** @alias EnsSPredictionexon
** @alias EnsOPredictionexon
**
** @attr Use [ajuint] Use counter
** @cc Bio::EnsEMBL::Storable
** @attr Identifier [ajuint] Internal SQL database identifier (primary key)
** @attr Adaptor [EnsPPredictionexonadaptor] Ensembl Prediction Exon Adaptor
** @cc Bio::EnsEMBL::Feature
** @attr Feature [EnsPFeature] Ensembl Feature
** @cc Bio::EnsEMBL::PredictionExon
** @cc 'prediction_exon' SQL table
** @attr Score [double] Score
** @attr Pvalue [double] P-value
** @attr PhaseStart [ajint] Start phase
** @attr Padding [char[4]] Padding to alignment boundary
** @attr SequenceCache [AjPStr] Sequence cache
** @@
******************************************************************************/

typedef struct EnsSPredictionexon
{
    ajuint Use;
    ajuint Identifier;
    EnsPPredictionexonadaptor Adaptor;
    EnsPFeature Feature;
    double Score;
    double Pvalue;
    ajint PhaseStart;
    char Padding[4];
    AjPStr SequenceCache;
} EnsOPredictionexon;

#define EnsPPredictionexon EnsOPredictionexon*




/* @data EnsPPredictiontranscript *********************************************
**
** Ensembl Prediction Transcript.
**
** @alias EnsSPredictiontranscript
** @alias EnsOPredictiontranscript
**
** @attr Use [ajuint] Use counter
** @cc Bio::EnsEMBL::Storable
** @attr Identifier [ajuint] SQL database-internal identifier
** @attr Adaptor [EnsPPredictiontranscriptadaptor] Ensembl Prediction
**                                                 Transcript Adaptor
** @cc Bio::EnsEMBL::Feature
** @attr Feature [EnsPFeature] Ensembl Feature
** @cc Bio::EnsEMBL::PredictionTranscript
** @attr Displaylabel [AjPStr] Display label
** @attr Predictionexons [AjPList] AJAX List of Ensembl Prediction Exon objects
** @@
******************************************************************************/

typedef struct EnsSPredictiontranscript
{
    ajuint Use;
    ajuint Identifier;
    EnsPPredictiontranscriptadaptor Adaptor;
    EnsPFeature Feature;
    AjPStr Displaylabel;
    AjPList Predictionexons;
} EnsOPredictiontranscript;

#define EnsPPredictiontranscript EnsOPredictiontranscript*




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

/*
** Prototype definitions
*/

/* Ensembl Prediction Exon */

EnsPPredictionexon ensPredictionexonNewCpy(const EnsPPredictionexon pe);

EnsPPredictionexon ensPredictionexonNewIni(EnsPPredictionexonadaptor pea,
                                           ajuint identifier,
                                           EnsPFeature feature,
                                           ajint sphase,
                                           double score,
                                           double pvalue);

EnsPPredictionexon ensPredictionexonNewRef(EnsPPredictionexon pe);

void ensPredictionexonDel(EnsPPredictionexon* Ppe);

EnsPPredictionexonadaptor ensPredictionexonGetAdaptor(
    const EnsPPredictionexon pe);

EnsPFeature ensPredictionexonGetFeature(const EnsPPredictionexon pe);

ajuint ensPredictionexonGetIdentifier(const EnsPPredictionexon pe);

ajint ensPredictionexonGetPhaseStart(const EnsPPredictionexon pe);

double ensPredictionexonGetPvalue(const EnsPPredictionexon pe);

double ensPredictionexonGetScore(const EnsPPredictionexon pe);

AjBool ensPredictionexonSetAdaptor(EnsPPredictionexon pe,
                                   EnsPPredictionexonadaptor pea);

AjBool ensPredictionexonSetFeature(EnsPPredictionexon pe,
                                   EnsPFeature feature);

AjBool ensPredictionexonSetIdentifier(EnsPPredictionexon pe,
                                      ajuint identifier);

AjBool ensPredictionexonSetPhaseStart(EnsPPredictionexon pe,
                                      ajint sphase);

AjBool ensPredictionexonSetPvalue(EnsPPredictionexon pe,
                                  double pvalue);

AjBool ensPredictionexonSetScore(EnsPPredictionexon pe,
                                 double score);

AjBool ensPredictionexonTrace(const EnsPPredictionexon pe, ajuint level);

ajint ensPredictionexonGetPhaseEnd(const EnsPPredictionexon pe);

size_t ensPredictionexonCalculateMemsize(const EnsPPredictionexon pe);

EnsPPredictionexon ensPredictionexonTransfer(EnsPPredictionexon pe,
                                             EnsPSlice slice);

EnsPPredictionexon ensPredictionexonTransform(EnsPPredictionexon pe,
                                              const AjPStr csname,
                                              const AjPStr csversion);

AjBool ensPredictionexonFetchSequenceSeq(EnsPPredictionexon pe,
                                         AjPSeq* Psequence);

AjBool ensPredictionexonFetchSequenceStr(EnsPPredictionexon pe,
                                         AjPStr* Psequence);

AjBool ensListPredictionexonSortStartAscending(AjPList pes);

AjBool ensListPredictionexonSortStartDescending(AjPList pes);

/* Ensembl Prediction Exon Adaptor */

EnsPPredictionexonadaptor ensRegistryGetPredictionexonadaptor(
    EnsPDatabaseadaptor dba);

EnsPPredictionexonadaptor ensPredictionexonadaptorNew(
    EnsPDatabaseadaptor dba);

void ensPredictionexonadaptorDel(EnsPPredictionexonadaptor* Ppea);

EnsPDatabaseadaptor ensPredictionexonadaptorGetDatabaseadaptor(
    EnsPPredictionexonadaptor pea);

EnsPFeatureadaptor ensPredictionexonadaptorGetFeatureadaptor(
    EnsPPredictionexonadaptor pea);

AjBool ensPredictionexonadaptorFetchAllbyPredictiontranscript(
    EnsPPredictionexonadaptor pea,
    const EnsPPredictiontranscript pt,
    AjPList pes);

/* Ensembl Prediction Transcript */

EnsPPredictiontranscript ensPredictiontranscriptNewCpy(
    const EnsPPredictiontranscript pt);

EnsPPredictiontranscript ensPredictiontranscriptNewIni(
    EnsPPredictiontranscriptadaptor pta,
    ajuint identifier,
    EnsPFeature feature,
    AjPStr label);

EnsPPredictiontranscript ensPredictiontranscriptNewRef(
    EnsPPredictiontranscript pt);

void ensPredictiontranscriptDel(
    EnsPPredictiontranscript* Ppt);

EnsPPredictiontranscriptadaptor ensPredictiontranscriptGetAdaptor(
    const EnsPPredictiontranscript pt);

AjPStr ensPredictiontranscriptGetDisplaylabel(
    const EnsPPredictiontranscript pt);

EnsPFeature ensPredictiontranscriptGetFeature(
    const EnsPPredictiontranscript pt);

ajuint ensPredictiontranscriptGetIdentifier(
    const EnsPPredictiontranscript pt);

const AjPList ensPredictiontranscriptLoadPredictionexons(
    EnsPPredictiontranscript pt);

AjBool ensPredictiontranscriptSetAdaptor(
    EnsPPredictiontranscript pt,
    EnsPPredictiontranscriptadaptor pta);

AjBool ensPredictiontranscriptSetDisplaylabel(
    EnsPPredictiontranscript pt,
    AjPStr label);

AjBool ensPredictiontranscriptSetFeature(
    EnsPPredictiontranscript pt,
    EnsPFeature feature);

AjBool ensPredictiontranscriptSetIdentifier(
    EnsPPredictiontranscript pt,
    ajuint identifier);

AjBool ensPredictiontranscriptTrace(
    const EnsPPredictiontranscript pt,
    ajuint level);

size_t ensPredictiontranscriptCalculateMemsize(
    const EnsPPredictiontranscript pt);

ajint ensPredictiontranscriptCalculateSliceCodingEnd(
    const EnsPPredictiontranscript pt);

ajint ensPredictiontranscriptCalculateSliceCodingStart(
    const EnsPPredictiontranscript pt);

ajuint ensPredictiontranscriptCalculateTranscriptCodingEnd(
    EnsPPredictiontranscript pt);

ajuint ensPredictiontranscriptCalculateTranscriptCodingStart(
    const EnsPPredictiontranscript pt);

AjBool ensPredictiontranscriptFetchSequenceTranscriptSeq(
    EnsPPredictiontranscript pt,
    AjPSeq* Psequence);

AjBool ensPredictiontranscriptFetchSequenceTranscriptStr(
    EnsPPredictiontranscript pt,
    AjPStr* Psequence);

AjBool ensPredictiontranscriptFetchSequenceTranslationSeq(
    EnsPPredictiontranscript pt,
    AjPSeq* Psequence);

AjBool ensPredictiontranscriptFetchSequenceTranslationStr(
    EnsPPredictiontranscript pt,
    AjPStr* Psequence);

EnsPPredictiontranscript ensPredictiontranscriptTransfer(
    EnsPPredictiontranscript pt,
    EnsPSlice slice);

EnsPPredictiontranscript ensPredictiontranscriptTransform(
    EnsPPredictiontranscript pt,
    const AjPStr csname,
    const AjPStr csversion);

AjBool ensListPredictiontranscriptSortStartAscending(AjPList pts);

AjBool ensListPredictiontranscriptSortStartDescending(AjPList pts);

/* Ensembl Prediction Transcript Adaptor */

EnsPPredictiontranscriptadaptor ensRegistryGetPredictiontranscriptadaptor(
    EnsPDatabaseadaptor dba);

EnsPPredictiontranscriptadaptor ensPredictiontranscriptadaptorNew(
    EnsPDatabaseadaptor dba);

void ensPredictiontranscriptadaptorDel(
    EnsPPredictiontranscriptadaptor* Ppta);

EnsPDatabaseadaptor ensPredictiontranscriptadaptorGetDatabaseadaptor(
    EnsPPredictiontranscriptadaptor pta);

EnsPFeatureadaptor ensPredictiontranscriptadaptorGetFeatureadaptor(
    EnsPPredictiontranscriptadaptor pta);

AjBool ensPredictiontranscriptadaptorFetchByIdentifier(
    EnsPPredictiontranscriptadaptor pta,
    ajuint identifier,
    EnsPPredictiontranscript* Ppt);

AjBool ensPredictiontranscriptadaptorFetchByStableidentifier(
    EnsPPredictiontranscriptadaptor pta,
    const AjPStr stableid,
    EnsPPredictiontranscript* Ppt);

/*
** End of prototype definitions
*/




AJ_END_DECLS

#endif /* !ENSPREDICTION_H */