/usr/lib/emboss/include/ensfeature.h is in emboss-lib 6.3.1-6ubuntu3.
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extern "C"
{
#endif
#ifndef ensfeature_h
#define ensfeature_h
#include "ensdata.h"
#include "ensassemblyexception.h"
#include "ensdatabaseentry.h"
#include "ensmetainformation.h"
#include "ensmetacoordinate.h"
#include "ensslice.h"
/* @data EnsPFeaturepair ******************************************************
**
** Ensembl Feature Pair.
**
** @alias EnsSFeaturepair
** @alias EnsOFeaturepair
**
** @cc Bio::EnsEMBL::Featurepair
** @attr SourceFeature [EnsPFeature] Source Ensembl Feature (Query)
** @attr TargetFeature [EnsPFeature] Target Ensembl Feature (Target)
** @attr Externaldatabase [EnsPExternaldatabase] Ensembl External Database
** @attr ExtraData [AjPStr] Extra data
** @attr SourceSpecies [AjPStr] Source species name
** @attr TargetSpecies [AjPStr] Target species name
** @attr GroupIdentifier [ajuint] Group identifier
** @attr LevelIdentifier [ajuint] Level identifier
** @attr Evalue [double] e- or p-value
** @attr Score [double] Score
** @attr SourceCoverage [float] Source coverage in percent
** @attr TargetCoverage [float] Target coverage in percent
** @attr SequenceIdentity [float] Sequence identity in percent
** @attr Use [ajuint] Use counter
** @@
******************************************************************************/
typedef struct EnsSFeaturepair
{
EnsPFeature SourceFeature;
EnsPFeature TargetFeature;
EnsPExternaldatabase Externaldatabase;
AjPStr ExtraData;
AjPStr SourceSpecies;
AjPStr TargetSpecies;
ajuint GroupIdentifier;
ajuint LevelIdentifier;
double Evalue;
double Score;
float SourceCoverage;
float TargetCoverage;
float SequenceIdentity;
ajuint Use;
} EnsOFeaturepair;
#define EnsPFeaturepair EnsOFeaturepair*
/* @data EnsPDNAAlignFeatureadaptor *******************************************
**
** Ensembl DNA Align Feature Adaptor.
**
** @alias EnsSDNAAlignFeatureadaptor
** @alias EnsODNAAlignFeatureadaptor
**
** @attr Adaptor [EnsPFeatureadaptor] Ensembl Feature Adaptor
** @@
******************************************************************************/
typedef struct EnsSDNAAlignFeatureadaptor
{
EnsPFeatureadaptor Adaptor;
} EnsODNAAlignFeatureadaptor;
#define EnsPDNAAlignFeatureadaptor EnsODNAAlignFeatureadaptor*
/* @data EnsPProteinalignfeatureadaptor ***************************************
**
** Ensembl Protein Align Feature Adaptor.
**
** @alias EnsSProteinalignfeatureadaptor
** @alias EnsOProteinalignfeatureadaptor
**
** @attr Adaptor [EnsPFeatureadaptor] Ensembl Feature Adaptor
** @@
******************************************************************************/
typedef struct EnsSProteinalignfeatureadaptor
{
EnsPFeatureadaptor Adaptor;
} EnsOProteinalignfeatureadaptor;
#define EnsPProteinalignfeatureadaptor EnsOProteinalignfeatureadaptor*
/* EnsEBasealignfeatureType ***************************************************
**
** Ensembl Base Align Feature Type enumeration.
**
******************************************************************************/
typedef enum EnsOBasealignfeatureType
{
ensEBasealignfeatureTypeNULL,
ensEBasealignfeatureTypeDNA,
ensEBasealignfeatureTypeProtein
} EnsEBasealignfeatureType;
/* @data EnsPBasealignfeature *************************************************
**
** Ensembl Base Align Feature.
**
** @alias EnsSBasealignfeature
** @alias EnsOBasealignfeature
**
** @attr Use [ajuint] Use counter
** @cc Bio::EnsEMBL::Storable
** @attr Identifier [ajuint] SQL database-internal identifier
** @attr DNAAlignFeatureadaptor [EnsPDNAAlignFeatureadaptor]
** Ensembl DNA Align Feature Adaptor
** @attr Proteinalignfeatureadaptor [EnsPProteinalignfeatureadaptor]
** Ensembl Protein Align Feature Adaptor
** @cc Bio::EnsEMBL::Featurepair
** @attr Featurepair [EnsPFeaturepair] Ensembl Feature Pair
** @cc Bio::EnsEMBL::Basealignfeature
** @attr GetFeaturepair [(EnsPFeaturepair*)] Get Ensembl Feature Pair function
** @attr Cigar [AjPStr] CIGAR line
** @attr Type [EnsEBasealignfeatureType] Type
** @attr AlignmentLength [ajuint] Target component alignment length
** @attr PairDNAAlignFeatureIdentifier [ajuint] Pair DNA Align Feature
** identifier
** @attr Padding [ajuint] Padding to alignment boundary
** @@
******************************************************************************/
typedef struct EnsSBasealignfeature
{
ajuint Use;
ajuint Identifier;
EnsPDNAAlignFeatureadaptor DNAAlignFeatureadaptor;
EnsPProteinalignfeatureadaptor Proteinalignfeatureadaptor;
EnsPFeaturepair Featurepair;
EnsPFeaturepair (*GetFeaturepair)(void* object);
AjPStr Cigar;
EnsEBasealignfeatureType Type;
ajuint AlignmentLength;
ajuint PairDNAAlignFeatureIdentifier;
ajuint Padding;
} EnsOBasealignfeature;
#define EnsPBasealignfeature EnsOBasealignfeature*
/* @data EnsPProteinfeatureadaptor ********************************************
**
** Ensembl Protein Feature Adaptor.
**
** @alias EnsSProteinfeatureadaptor
** @alias EnsOProteinfeatureadaptor
**
** @attr Adaptor [EnsPBaseadaptor] Ensembl Base Adaptor
** @@
******************************************************************************/
typedef struct EnsSProteinfeatureadaptor
{
EnsPBaseadaptor Adaptor;
} EnsOProteinfeatureadaptor;
#define EnsPProteinfeatureadaptor EnsOProteinfeatureadaptor*
/* @data EnsPProteinfeature ***************************************************
**
** Ensembl Protein Feature.
**
** @alias EnsSProteinfeature
** @alias EnsOProteinfeature
**
** @attr Use [ajuint] Use counter
** @cc Bio::EnsEMBL::Storable
** @attr Identifier [ajuint] SQL database-internal identifier
** @attr Adaptor [EnsPProteinfeatureadaptor] Ensembl Protein Feature Adaptor
** @cc Bio::EnsEMBL::Featurepair
** @attr Featurepair [EnsPFeaturepair] Ensembl Feature Pair
** @cc Bio::EnsEMBL::Proteinfeature
** @attr Accession [AjPStr] (InterPro) Accession
** @attr Description [AjPStr] (InterPro) Description
** @@
******************************************************************************/
typedef struct EnsSProteinfeature
{
ajuint Use;
ajuint Identifier;
EnsPProteinfeatureadaptor Adaptor;
EnsPFeaturepair Featurepair;
AjPStr Accession;
AjPStr Description;
} EnsOProteinfeature;
#define EnsPProteinfeature EnsOProteinfeature*
/* @data EnsPSimplefeatureadaptor *********************************************
**
** Ensembl Simple Feature Adaptor.
**
** @alias EnsSSimplefeatureadaptor
** @alias EnsOSimplefeatureadaptor
**
** @attr Adaptor [EnsPFeatureadaptor] Ensembl Feature Adaptor
** @@
******************************************************************************/
typedef struct EnsSSimplefeatureadaptor
{
EnsPFeatureadaptor Adaptor;
} EnsOSimplefeatureadaptor;
#define EnsPSimplefeatureadaptor EnsOSimplefeatureadaptor*
/* @data EnsPSimplefeature ****************************************************
**
** Ensembl Simple Feature.
**
** @alias EnsSSimplefeature
** @alias EnsOSimplefeature
**
** @attr Use [ajuint] Use counter
** @cc Bio::EnsEMBL::Storable
** @attr Identifier [ajuint] SQL database-internal identifier
** @attr Adaptor [EnsPSimplefeatureadaptor] Ensembl Simple Feature Adaptor
** @cc Bio::EnsEMBL::Feature
** @attr Feature [EnsPFeature] Ensembl Feature
** @cc Bio::EnsEMBL::Simplefeature
** @attr DisplayLabel [AjPStr] Display label
** @attr Score [double] Score
** @@
******************************************************************************/
typedef struct EnsSSimplefeature
{
ajuint Use;
ajuint Identifier;
EnsPSimplefeatureadaptor Adaptor;
EnsPFeature Feature;
AjPStr DisplayLabel;
double Score;
} EnsOSimplefeature;
#define EnsPSimplefeature EnsOSimplefeature*
/* @data EnsPAssemblyexceptionfeatureadaptor **********************************
**
** Ensembl Assembly Exception Feature Adaptor.
**
** @alias EnsSAssemblyexceptionfeatureadaptor
** @alias EnsOAssemblyexceptionfeatureadaptor
**
** @attr Adaptor [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @attr Cache [AjPList] AJAX List of Ensembl Assembly Exception Features
** @attr CacheByIdentifier [AjPTable] AJAX Table of Ensembl Assembly Exception
** Features
** @attr CacheBySlice [EnsPCache] Ensembl Cache by Ensembl Slice names
** @@
******************************************************************************/
typedef struct EnsSAssemblyexceptionfeatureadaptor
{
EnsPDatabaseadaptor Adaptor;
AjPList Cache;
AjPTable CacheByIdentifier;
EnsPCache CacheBySlice;
} EnsOAssemblyexceptionfeatureadaptor;
#define EnsPAssemblyexceptionfeatureadaptor EnsOAssemblyexceptionfeatureadaptor*
/* @data EnsPAssemblyexceptionfeature *****************************************
**
** Ensembl Assembly Exception Feature.
**
** @alias EnsSAssemblyexceptionfeature
** @alias EnsOAssemblyexceptionfeature
**
** @attr Use [ajuint] Use counter
** @cc Bio::EnsEMBL::Storable
** @attr Identifier [ajuint] SQL database-internal identifier
** @attr Adaptor [EnsPAssemblyexceptionfeatureadaptor]
** Ensembl Assembly Exception Feature Adaptor
** @cc Bio::EnsEMBL::Feature
** @attr Feature [EnsPFeature] Ensembl Feature
** @cc Bio::EnsEMBL::Assemblyexceptionfeature
** @attr AlternateSlice [EnsPSlice] Alternate Ensembl Slice
** @attr Type [EnsEAssemblyexceptionType] Ensembl Assembly Exception type
** @attr Padding [ajuint] Padding to alignment boundary
** @@
******************************************************************************/
typedef struct EnsSAssemblyexceptionfeature
{
ajuint Use;
ajuint Identifier;
EnsPAssemblyexceptionfeatureadaptor Adaptor;
EnsPFeature Feature;
EnsPSlice AlternateSlice;
EnsEAssemblyexceptionType Type;
ajuint Padding;
} EnsOAssemblyexceptionfeature;
#define EnsPAssemblyexceptionfeature EnsOAssemblyexceptionfeature*
/*
** Prototype definitions
*/
/* Ensembl Feature */
EnsPFeature ensFeatureNewS(EnsPAnalysis analysis,
EnsPSlice slice,
ajint start,
ajint end,
ajint strand);
EnsPFeature ensFeatureNewN(EnsPAnalysis analysis,
AjPStr seqname,
ajint start,
ajint end,
ajint strand);
EnsPFeature ensFeatureNewObj(const EnsPFeature object);
EnsPFeature ensFeatureNewRef(EnsPFeature feature);
void ensFeatureDel(EnsPFeature* Pfeature);
EnsPAnalysis ensFeatureGetAnalysis(const EnsPFeature feature);
EnsPSlice ensFeatureGetSlice(const EnsPFeature feature);
AjPStr ensFeatureGetSequenceName(const EnsPFeature feature);
ajint ensFeatureGetStart(const EnsPFeature feature);
ajint ensFeatureGetEnd(const EnsPFeature feature);
ajint ensFeatureGetStrand(const EnsPFeature feature);
AjBool ensFeatureSetAnalysis(EnsPFeature feature, EnsPAnalysis analysis);
AjBool ensFeatureSetSlice(EnsPFeature feature, EnsPSlice slice);
AjBool ensFeatureSetSequenceName(EnsPFeature, AjPStr seqname);
AjBool ensFeatureSetStart(EnsPFeature feature, ajint start);
AjBool ensFeatureSetEnd(EnsPFeature feature, ajint end);
AjBool ensFeatureSetStrand(EnsPFeature feature, ajint strand);
AjBool ensFeatureTrace(const EnsPFeature feature, ajuint level);
ajuint ensFeatureGetLength(const EnsPFeature feature);
ajulong ensFeatureGetMemsize(const EnsPFeature feature);
const EnsPSeqregion ensFeatureGetSeqregion(const EnsPFeature feature);
ajint ensFeatureGetSeqregionStart(const EnsPFeature feature);
ajint ensFeatureGetSeqregionEnd(const EnsPFeature feature);
ajint ensFeatureGetSeqregionStrand(const EnsPFeature feature);
const AjPStr ensFeatureGetSeqregionName(const EnsPFeature feature);
ajuint ensFeatureGetSeqregionLength(const EnsPFeature feature);
AjBool ensFeatureMove(EnsPFeature feature,
ajint start,
ajint end,
ajint strand);
AjBool ensFeatureProject(const EnsPFeature feature,
const AjPStr csname,
const AjPStr csversion,
AjPList pss);
EnsPFeature ensFeatureTransform(EnsPFeature feature,
const AjPStr csname,
const AjPStr csversion);
EnsPFeature ensFeatureTransfer(EnsPFeature feature, EnsPSlice slice);
AjBool ensFeatureFetchAllAlternativeLocations(EnsPFeature feature,
AjBool all,
AjPList features);
int ensFeatureCompareStartAscending(const EnsPFeature feature1,
const EnsPFeature feature2);
int ensFeatureCompareStartDescending(const EnsPFeature feature1,
const EnsPFeature feature2);
AjBool ensFeatureSortByStartAscending(AjPList features);
AjBool ensFeatureSortByStartDescending(AjPList features);
AjBool ensFeatureMatch(const EnsPFeature feature1,
const EnsPFeature feature2);
AjBool ensFeatureOverlap(const EnsPFeature feature1,
const EnsPFeature feature2);
AjBool ensFeatureFetchSeqregionName(const EnsPFeature feature, AjPStr* Pname);
/* Ensembl Feature Adaptor */
EnsPFeatureadaptor ensFeatureadaptorNew(
EnsPDatabaseadaptor dba,
const char **Ptables,
const char **Pcolumns,
EnsOBaseadaptorLeftJoin *leftjoin,
const char *condition,
const char *final,
AjBool Fquery(EnsPDatabaseadaptor dba,
const AjPStr statement,
EnsPAssemblymapper am,
EnsPSlice slice,
AjPList objects),
void* Fread(const void* key),
void* Freference(void* value),
AjBool Fwrite(const void* value),
void Fdelete(void** value),
ajulong Fsize(const void* value),
EnsPFeature Fgetfeature(const void *object),
const char *label);
void ensFeatureadaptorDel(EnsPFeatureadaptor *Pfa);
EnsPBaseadaptor ensFeatureadaptorGetBaseadaptor(const EnsPFeatureadaptor fa);
EnsPCache ensFeatureadaptorGetCache(const EnsPFeatureadaptor fa);
ajuint ensFeatureadaptorGetMaxFeatureLength(const EnsPFeatureadaptor fa);
EnsPDatabaseadaptor ensFeatureadaptorGetDatabaseadaptor(
const EnsPFeatureadaptor fa);
AjBool ensFeatureadaptorSetMaximumFeatureLength(EnsPFeatureadaptor fa,
ajuint length);
AjBool ensFeatureadaptorSetTables(EnsPFeatureadaptor fa,
const char **Ptables);
AjBool ensFeatureadaptorSetColumns(EnsPFeatureadaptor fa,
const char **Pcolumns);
AjBool ensFeatureadaptorSetDefaultCondition(EnsPFeatureadaptor fa,
const char *condition);
AjBool ensFeatureadaptorSetFinalCondition(EnsPFeatureadaptor fa,
const char *final);
AjBool ensFeatureadaptorEscapeC(EnsPFeatureadaptor fa,
char **Ptxt,
const AjPStr str);
AjBool ensFeatureadaptorEscapeS(EnsPFeatureadaptor fa,
AjPStr *Pstr,
const AjPStr str);
AjBool ensFeatureadaptorFetchAllBySliceConstraint(EnsPFeatureadaptor fa,
EnsPSlice slice,
const AjPStr constraint,
const AjPStr anname,
AjPList objects);
AjBool ensFeatureadaptorFetchAllBySlice(EnsPFeatureadaptor fa,
EnsPSlice slice,
const AjPStr anname,
AjPList objects);
AjBool ensFeatureadaptorFetchAllBySliceScore(EnsPFeatureadaptor fa,
EnsPSlice slice,
double score,
const AjPStr anname,
AjPList objects);
AjBool ensFeatureadaptorFetchAllByAnalysisName(EnsPFeatureadaptor fa,
const AjPStr anname,
AjPList objects);
/* Ensembl Feature Pair */
EnsPFeaturepair ensFeaturepairNew(EnsPFeature srcfeature,
EnsPFeature trgfeature,
EnsPExternaldatabase edb,
AjPStr extra,
AjPStr srcspecies,
AjPStr trgspecies,
ajuint groupid,
ajuint levelid,
double evalue,
double score,
float srccoverage,
float trgcoverage,
float identity);
EnsPFeaturepair ensFeaturepairNewObj(const EnsPFeaturepair object);
EnsPFeaturepair ensFeaturepairNewRef(EnsPFeaturepair fp);
void ensFeaturepairDel(EnsPFeaturepair* Pfp);
EnsPFeature ensFeaturepairGetSourceFeature(const EnsPFeaturepair fp);
EnsPFeature ensFeaturepairGetTargetFeature(const EnsPFeaturepair fp);
EnsPExternaldatabase ensFeaturepairGetExternaldatabase(
const EnsPFeaturepair fp);
AjPStr ensFeaturepairGetExtraData(const EnsPFeaturepair fp);
AjPStr ensFeaturepairGetSourceSpecies(const EnsPFeaturepair fp);
AjPStr ensFeaturepairGetTargetSpecies(const EnsPFeaturepair fp);
ajuint ensFeaturepairGetGroupIdentifier(const EnsPFeaturepair fp);
ajuint ensFeaturepairGetLevelIdentifier(const EnsPFeaturepair fp);
double ensFeaturepairGetEvalue(const EnsPFeaturepair fp);
double ensFeaturepairGetScore(const EnsPFeaturepair fp);
float ensFeaturepairGetSourceCoverage(const EnsPFeaturepair fp);
float ensFeaturepairGetTargetCoverage(const EnsPFeaturepair fp);
float ensFeaturepairGetSequenceIdentity(const EnsPFeaturepair fp);
AjBool ensFeaturepairSetSourceFeature(EnsPFeaturepair fp, EnsPFeature feature);
AjBool ensFeaturepairSetTargetFeature(EnsPFeaturepair fp, EnsPFeature feature);
AjBool ensFeaturepairSetExternaldatabase(EnsPFeaturepair fp,
EnsPExternaldatabase edb);
AjBool ensFeaturepairSetExtraData(EnsPFeaturepair fp, AjPStr extra);
AjBool ensFeaturepairSetSourceSpecies(EnsPFeaturepair fp, AjPStr species);
AjBool ensFeaturepairSetTargetSpecies(EnsPFeaturepair fp, AjPStr species);
AjBool ensFeaturepairSetGroupIdentifier(EnsPFeaturepair fp, ajuint groupid);
AjBool ensFeaturepairSetLevelIdentifier(EnsPFeaturepair fp, ajuint levelid);
AjBool ensFeaturepairSetEvalue(EnsPFeaturepair fp, double evalue);
AjBool ensFeaturepairSetScore(EnsPFeaturepair fp, double score);
AjBool ensFeaturepairSetSourceCoverage(EnsPFeaturepair fp, float coverage);
AjBool ensFeaturepairSetTargetCoverage(EnsPFeaturepair fp, float coverage);
AjBool ensFeaturepairTrace(const EnsPFeaturepair fp, ajuint level);
AjBool ensFeaturepairSetSequenceIdentity(EnsPFeaturepair fp, float identity);
ajulong ensFeaturepairGetMemsize(const EnsPFeaturepair fp);
EnsPFeaturepair ensFeaturepairTransform(const EnsPFeaturepair fp,
const AjPStr csname,
const AjPStr csversion);
EnsPFeaturepair ensFeaturepairTransfer(EnsPFeaturepair fp, EnsPSlice slice);
int ensFeaturepairCompareSourceFeatureStartAscending(const void* P1,
const void* P2);
int ensFeaturepairCompareSourceFeatureStartDescending(const void* P1,
const void* P2);
AjBool ensFeaturepairSortBySourceFeatureStartAscending(AjPList fps);
AjBool ensFeaturepairSortBySourceFeatureStartDescending(AjPList fps);
/* Ensembl Base Align Feature */
EnsPBasealignfeature ensBasealignfeatureNewD(
EnsPDNAAlignFeatureadaptor dafa,
ajuint identifier,
EnsPFeaturepair fp,
AjPStr cigar,
ajuint pair);
EnsPBasealignfeature ensBasealignfeatureNewP(
EnsPProteinalignfeatureadaptor pafa,
ajuint identifier,
EnsPFeaturepair fp,
AjPStr cigar);
EnsPBasealignfeature ensBasealignfeatureNew(
EnsPFeaturepair fp,
AjPStr cigar,
AjPList fps,
EnsEBasealignfeatureType type,
ajuint pair);
EnsPBasealignfeature ensBasealignfeatureNewObj(
const EnsPBasealignfeature object);
EnsPBasealignfeature ensBasealignfeatureNewRef(EnsPBasealignfeature baf);
void ensBasealignfeatureDel(EnsPBasealignfeature *Pbaf);
EnsPDNAAlignFeatureadaptor ensBasealignfeatureGetDNAAlignFeatureadaptor(
const EnsPBasealignfeature baf);
EnsPProteinalignfeatureadaptor ensBasealignfeatureGetProteinalignfeatureadaptor(
const EnsPBasealignfeature baf);
ajuint ensBasealignfeatureGetIdentifier(const EnsPBasealignfeature baf);
EnsPFeaturepair ensBasealignfeatureGetFeaturepair(
const EnsPBasealignfeature baf);
AjBool ensBasealignfeatureSetFeaturepair(EnsPBasealignfeature baf,
EnsPFeaturepair fp);
EnsPFeature ensBasealignfeatureGetFeature(const EnsPBasealignfeature baf);
ajuint ensBasealignfeatureGetAlignmentLength(EnsPBasealignfeature baf);
void *ensBasealignfeatureGetAdaptor(const EnsPBasealignfeature baf);
ajuint ensBasealignfeatureGetSourceUnit(const EnsPBasealignfeature baf);
ajuint ensBasealignfeatureGetTargetUnit(const EnsPBasealignfeature baf);
ajulong ensBasealignfeatureGetMemsize(const EnsPBasealignfeature baf);
EnsPBasealignfeature ensBasealignfeatureTransform(
const EnsPBasealignfeature baf,
const AjPStr csname,
const AjPStr csversion);
EnsPBasealignfeature ensBasealignfeatureTransfer(EnsPBasealignfeature baf,
EnsPSlice slice);
AjBool ensBasealignfeatureTrace(const EnsPBasealignfeature baf, ajuint level);
AjBool ensBasealignfeatureFetchAllFeaturepairs(const EnsPBasealignfeature baf,
AjPList fps);
AjBool ensBasealignfeatureSortBySourceFeatureStartAscending(AjPList bafs);
AjBool ensBasealignfeatureSortBySourceFeatureStartDescending(AjPList bafs);
/* Ensembl DNA Align Feature Adaptor */
EnsPDNAAlignFeatureadaptor ensRegistryGetDNAAlignFeatureadaptor(
EnsPDatabaseadaptor dba);
EnsPDNAAlignFeatureadaptor ensDNAAlignFeatureadaptorNew(
EnsPDatabaseadaptor dba);
void ensDNAAlignFeatureadaptorDel(EnsPDNAAlignFeatureadaptor *Pdafa);
AjBool ensDNAAlignFeatureadaptorFetchByIdentifier(
EnsPDNAAlignFeatureadaptor dafa,
ajuint identifier,
EnsPBasealignfeature *Pbaf);
AjBool ensDNAAlignFeatureadaptorFetchAllBySliceIdentity(
EnsPDNAAlignFeatureadaptor dafa,
EnsPSlice slice,
float identity,
const AjPStr anname,
AjPList bafs);
AjBool ensDNAAlignFeatureadaptorFetchAllBySliceCoverage(
EnsPDNAAlignFeatureadaptor dafa,
EnsPSlice slice,
float coverage,
const AjPStr anname,
AjPList bafs);
AjBool ensDNAAlignFeatureadaptorFetchAllBySliceExternaldatabase(
EnsPDNAAlignFeatureadaptor dafa,
EnsPSlice slice,
const AjPStr edbname,
const AjPStr anname,
AjPList bafs);
AjBool ensDNAAlignFeatureadaptorFetchAllByHitName(
EnsPDNAAlignFeatureadaptor dafa,
const AjPStr hitname,
const AjPStr anname,
AjPList bafs);
AjBool ensDNAAlignFeatureadaptorFetchAllByHitUnversioned(
EnsPDNAAlignFeatureadaptor dafa,
const AjPStr hitname,
const AjPStr anname,
AjPList bafs);
AjBool ensDNAAlignFeatureadaptorFetchAllIdentifiers(
EnsPDNAAlignFeatureadaptor dafa,
AjPList idlist);
/* Ensembl Protein Align Feature Adaptor */
EnsPProteinalignfeatureadaptor ensRegistryGetProteinalignfeatureadaptor(
EnsPDatabaseadaptor dba);
EnsPProteinalignfeatureadaptor ensProteinalignfeatureadaptorNew(
EnsPDatabaseadaptor dba);
void ensProteinalignfeatureadaptorDel(EnsPProteinalignfeatureadaptor *Ppafa);
AjBool ensProteinalignfeatureadaptorFetchByIdentifier(
EnsPProteinalignfeatureadaptor pafa,
ajuint identifier,
EnsPBasealignfeature *Pbaf);
AjBool ensProteinalignfeatureadaptorFetchAllBySliceIdentity(
EnsPProteinalignfeatureadaptor pafa,
EnsPSlice slice,
float identity,
const AjPStr anname,
AjPList bafs);
AjBool ensProteinalignfeatureadaptorFetchAllBySliceCoverage(
EnsPProteinalignfeatureadaptor pafa,
EnsPSlice slice,
float coverage,
const AjPStr anname,
AjPList bafs);
AjBool ensProteinalignfeatureadaptorFetchAllBySliceExternaldatabase(
EnsPProteinalignfeatureadaptor pafa,
EnsPSlice slice,
const AjPStr edbname,
const AjPStr anname,
AjPList bafs);
AjBool ensProteinalignfeatureadaptorFetchAllByHitName(
EnsPProteinalignfeatureadaptor pafa,
const AjPStr hitname,
const AjPStr anname,
AjPList bafs);
AjBool ensProteinalignfeatureadaptorFetchAllByHitUnversioned(
EnsPProteinalignfeatureadaptor pafa,
const AjPStr hitname,
const AjPStr anname,
AjPList bafs);
AjBool ensProteinalignfeatureadaptorFetchAllIdentifiers(
EnsPProteinalignfeatureadaptor pafa,
AjPList idlist);
/* Ensembl Protein Feature */
EnsPProteinfeature ensProteinfeatureNew(
EnsPProteinfeatureadaptor pfa,
ajuint identifier,
EnsPFeaturepair fp,
AjPStr accession,
AjPStr description);
EnsPProteinfeature ensProteinfeatureNewObj(const EnsPProteinfeature object);
EnsPProteinfeature ensProteinfeatureNewRef(EnsPProteinfeature pf);
void ensProteinfeatureDel(EnsPProteinfeature *Ppf);
EnsPProteinfeatureadaptor ensProteinfeatureGetAdaptor(
const EnsPProteinfeature pf);
ajuint ensProteinfeatureGetIdentifier(const EnsPProteinfeature pf);
EnsPFeaturepair ensProteinfeatureGetFeaturepair(const EnsPProteinfeature pf);
AjPStr ensProteinfeatureGetAccession(const EnsPProteinfeature pf);
AjPStr ensProteinfeatureGetDescription(const EnsPProteinfeature pf);
AjBool ensProteinfeatureSetAdaptor(EnsPProteinfeature pf,
EnsPProteinfeatureadaptor pfa);
AjBool ensProteinfeatureSetIdentifier(EnsPProteinfeature pf, ajuint identifier);
AjBool ensProteinfeatureSetFeaturepair(EnsPProteinfeature pf,
EnsPFeaturepair fp);
AjBool ensProteinfeatureSetAccession(EnsPProteinfeature pf, AjPStr accession);
AjBool ensProteinfeatureSetDescription(EnsPProteinfeature pf,
AjPStr description);
AjBool ensProteinfeatureTrace(const EnsPProteinfeature pf, ajuint level);
ajulong ensProteinfeatureGetMemsize(const EnsPProteinfeature pf);
/* Ensembl Protein Feature Adaptor */
EnsPProteinfeatureadaptor ensRegistryGetProteinfeatureadaptor(
EnsPDatabaseadaptor dba);
EnsPProteinfeatureadaptor ensProteinfeatureadaptorNew(
EnsPDatabaseadaptor dba);
void ensProteinfeatureadaptorDel(EnsPProteinfeatureadaptor *Ppfa);
AjBool ensProteinfeatureadaptorFetchAllByTranslationIdentifier(
EnsPProteinfeatureadaptor pfa,
ajuint tlid,
AjPList pfs);
AjBool ensProteinfeatureadaptorFetchByIdentifier(
EnsPProteinfeatureadaptor pfa,
ajuint identifier,
EnsPProteinfeature *Ppf);
/* Ensembl Simple Feature */
EnsPSimplefeature ensSimplefeatureNew(EnsPSimplefeatureadaptor pfa,
ajuint identifier,
EnsPFeature feature,
AjPStr label,
double score);
EnsPSimplefeature ensSimplefeatureNewObj(const EnsPSimplefeature object);
EnsPSimplefeature ensSimplefeatureNewRef(EnsPSimplefeature sf);
void ensSimplefeatureDel(EnsPSimplefeature* Psf);
EnsPSimplefeatureadaptor ensSimplefeatureGetAdaptor(const EnsPSimplefeature sf);
ajuint ensSimplefeatureGetIdentifier(const EnsPSimplefeature sf);
EnsPFeature ensSimplefeatureGetFeature(const EnsPSimplefeature sf);
AjPStr ensSimplefeatureGetDisplayLabel(const EnsPSimplefeature sf);
double ensSimplefeatureGetScore(const EnsPSimplefeature sf);
AjBool ensSimplefeatureSetAdaptor(EnsPSimplefeature sf,
EnsPSimplefeatureadaptor sfa);
AjBool ensSimplefeatureSetIdentifier(EnsPSimplefeature sf, ajuint identifier);
AjBool ensSimplefeatureSetFeature(EnsPSimplefeature sf, EnsPFeature feature);
AjBool ensSimplefeatureSetDisplayLabel(EnsPSimplefeature sf, AjPStr label);
AjBool ensSimplefeatureSetScore(EnsPSimplefeature sf, double score);
AjBool ensSimplefeatureTrace(const EnsPSimplefeature sf, ajuint level);
ajulong ensSimplefeatureGetMemsize(const EnsPSimplefeature sf);
AjBool ensSimplefeatureSortByStartAscending(AjPList sfs);
AjBool ensSimplefeatureSortByStartDescending(AjPList sfs);
/* Ensembl Simple Feature Adaptor */
EnsPSimplefeatureadaptor ensRegistryGetSimplefeatureadaptor(
EnsPDatabaseadaptor dba);
EnsPSimplefeatureadaptor ensSimplefeatureadaptorNew(
EnsPDatabaseadaptor dba);
void ensSimplefeatureadaptorDel(EnsPSimplefeatureadaptor *Psfa);
AjBool ensSimplefeatureadaptorFetchAllBySlice(EnsPSimplefeatureadaptor sfa,
EnsPSlice slice,
const AjPStr anname,
AjPList sfs);
AjBool ensSimplefeatureadaptorFetchAllBySliceScore(
EnsPSimplefeatureadaptor sfa,
EnsPSlice slice,
double score,
const AjPStr anname,
AjPList sfs);
AjBool ensSimplefeatureadaptorFetchAllByAnalysisName(
EnsPSimplefeatureadaptor sfa,
const AjPStr anname,
AjPList sfs);
/* Ensembl Assembly Exception Feature */
EnsPAssemblyexceptionfeature ensAssemblyexceptionfeatureNew(
EnsPAssemblyexceptionfeatureadaptor aefa,
ajuint identifier,
EnsPFeature feature,
EnsPSlice slice,
EnsEAssemblyexceptionType type);
EnsPAssemblyexceptionfeature ensAssemblyexceptionfeatureNewObj(
const EnsPAssemblyexceptionfeature object);
EnsPAssemblyexceptionfeature ensAssemblyexceptionfeatureNewRef(
EnsPAssemblyexceptionfeature aef);
void ensAssemblyexceptionfeatureDel(EnsPAssemblyexceptionfeature* Paef);
EnsPAssemblyexceptionfeatureadaptor ensAssemblyexceptionfeatureGetAdaptor(
const EnsPAssemblyexceptionfeature aef);
ajuint ensAssemblyexceptionfeatureGetIdentifier(
const EnsPAssemblyexceptionfeature aef);
EnsPFeature ensAssemblyexceptionfeatureGetFeature(
const EnsPAssemblyexceptionfeature aef);
EnsPSlice ensAssemblyexceptionfeatureGetAlternateSlice(
const EnsPAssemblyexceptionfeature aef);
EnsEAssemblyexceptionType ensAssemblyexceptionfeatureGetType(
const EnsPAssemblyexceptionfeature aef);
AjBool ensAssemblyexceptionfeatureSetAdaptor(
EnsPAssemblyexceptionfeature aef,
EnsPAssemblyexceptionfeatureadaptor aefa);
AjBool ensAssemblyexceptionfeatureSetIdentifier(
EnsPAssemblyexceptionfeature aef,
ajuint identifier);
AjBool ensAssemblyexceptionfeatureSetFeature(EnsPAssemblyexceptionfeature aef,
EnsPFeature feature);
AjBool ensAssemblyexceptionfeatureSetAlternateSlice(
EnsPAssemblyexceptionfeature aef,
EnsPSlice altslice);
AjBool ensAssemblyexceptionfeatureSetType(EnsPAssemblyexceptionfeature aef,
EnsEAssemblyexceptionType type);
AjBool ensAssemblyexceptionfeatureFetchDisplayIdentifier(
const EnsPAssemblyexceptionfeature aef,
AjPStr *Pidentifier);
AjBool ensAssemblyexceptionfeatureTrace(const EnsPAssemblyexceptionfeature aef,
ajuint level);
/* Ensembl Assembly Exception Feature Adaptor */
EnsPAssemblyexceptionfeatureadaptor ensRegistryGetAssemblyexceptionfeatureadaptor(
EnsPDatabaseadaptor dba);
EnsPAssemblyexceptionfeatureadaptor ensAssemblyexceptionfeatureadaptorNew(
EnsPDatabaseadaptor dba);
void ensAssemblyexceptionfeatureadaptorDel(
EnsPAssemblyexceptionfeatureadaptor* Paefa);
AjBool ensAssemblyexceptionfeatureadaptorFetchAll(
EnsPAssemblyexceptionfeatureadaptor aefa,
AjPList aefs);
AjBool ensAssemblyexceptionfeatureadaptorFetchByIdentifier(
EnsPAssemblyexceptionfeatureadaptor aefa,
ajuint identifier,
EnsPAssemblyexceptionfeature* Paef);
AjBool ensAssemblyexceptionfeatureadaptorFetchAllBySlice(
EnsPAssemblyexceptionfeatureadaptor aefa,
EnsPSlice slice,
AjPList aefs);
/*
** End of prototype definitions
*/
#endif /* ensfeature_h */
#ifdef __cplusplus
}
#endif
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