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/* @include ensditag **********************************************************
**
** Ensembl Ditag functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.24 $
** @modified 2009 by Alan Bleasby for incorporation into EMBOSS core
** @modified $Date: 2012/08/05 10:43:54 $ by $Author: mks $
** @@
**
** This library is free software; you can redistribute it and/or
** modify it under the terms of the GNU Lesser General Public
** License as published by the Free Software Foundation; either
** version 2.1 of the License, or (at your option) any later version.
**
** This library is distributed in the hope that it will be useful,
** but WITHOUT ANY WARRANTY; without even the implied warranty of
** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
** Lesser General Public License for more details.
**
** You should have received a copy of the GNU Lesser General Public
** License along with this library; if not, write to the Free Software
** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
** MA 02110-1301, USA.
**
******************************************************************************/
#ifndef ENSDITAG_H
#define ENSDITAG_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ensfeature.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* @const EnsPDitagadaptor ****************************************************
**
** Ensembl Ditag Adaptor.
** Defined as an alias in EnsPBaseadaptor.
**
** #alias EnsPBaseadaptor
**
** #cc Bio::EnsEMBL::Map::DBSQL::DitagAdaptor
** ##
******************************************************************************/
#define EnsPDitagadaptor EnsPBaseadaptor
/* @const EnsPDitagfeatureadaptor *********************************************
**
** Ensembl Ditag Feature Adaptor.
** Defined as an alias in EnsPFeatureadaptor.
**
** #alias EnsPFeatureadaptor
**
** #cc Bio::EnsEMBL::Map::DBSQL::Ditagfeatureadaptor
** ##
******************************************************************************/
#define EnsPDitagfeatureadaptor EnsPFeatureadaptor
/* @enum EnsEDitagfeatureSide *************************************************
**
** Ensembl Ditag Feature Side enumeration
**
** @value ensEDitagfeatureSideNULL Null
** @value ensEDitagfeatureSideLeft Left side
** @value ensEDitagfeatureSideRight Right side
** @value ensEDitagfeatureSideFull Full
** @@
******************************************************************************/
typedef enum EnsODitagfeatureSide
{
ensEDitagfeatureSideNULL,
ensEDitagfeatureSideLeft,
ensEDitagfeatureSideRight,
ensEDitagfeatureSideFull
} EnsEDitagfeatureSide;
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* @data EnsPDitag ************************************************************
**
** Ensembl Ditag
**
** @alias EnsSDitag
** @alias EnsODitag
**
** @attr Use [ajuint] Use counter
** @cc Bio::EnsEMBL::Storable
** @attr Identifier [ajuint] Internal SQL database identifier (primary key)
** @attr Adaptor [EnsPDitagadaptor] Ensembl Ditag Adaptor
** @cc Bio::EnsEMBL::Map::Ditag
** @attr Name [AjPStr] Name
** @attr Type [AjPStr] Source
** @attr Sequence [AjPStr] Sequence
** @attr Count [ajuint] Count
** @attr Padding [ajuint] Padding to alignment boundary
** @@
******************************************************************************/
typedef struct EnsSDitag
{
ajuint Use;
ajuint Identifier;
EnsPDitagadaptor Adaptor;
AjPStr Name;
AjPStr Type;
AjPStr Sequence;
ajuint Count;
ajuint Padding;
} EnsODitag;
#define EnsPDitag EnsODitag*
/* @data EnsPDitagfeature *****************************************************
**
** Ensembl Ditag Feature
**
** @alias EnsSDitagfeature
** @alias EnsODitagfeature
**
** @attr Use [ajuint] Use counter
** @cc Bio::EnsEMBL::Storable
** @attr Identifier [ajuint] Internal SQL database identifier (primary key)
** @attr Adaptor [EnsPDitagfeatureadaptor] Ensembl Ditag Feature Adaptor
** @cc Bio::EnsEMBL::Feature
** @attr Feature [EnsPFeature] Ensembl Feature
** @cc Bio::EnsEMBL::Map::DitagFeature
** @attr Ditag [EnsPDitag] Ditag
** @attr Cigar [AjPStr] CIGAR line
** @attr Side [EnsEDitagfeatureSide] Side
** @attr TargetStart [ajint] Target start
** @attr TargetEnd [ajint] Target end
** @attr TargetStrand [ajint] Target strand
** @attr Pairidentifier [ajuint] Pair identifier
** @attr Padding [ajuint] Padding to alignment boundary
** @@
******************************************************************************/
typedef struct EnsSDitagfeature
{
ajuint Use;
ajuint Identifier;
EnsPDitagfeatureadaptor Adaptor;
EnsPFeature Feature;
EnsPDitag Ditag;
AjPStr Cigar;
EnsEDitagfeatureSide Side;
ajint TargetStart;
ajint TargetEnd;
ajint TargetStrand;
ajuint Pairidentifier;
ajuint Padding;
} EnsODitagfeature;
#define EnsPDitagfeature EnsODitagfeature*
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
/* Ensembl Ditag */
EnsPDitag ensDitagNewCpy(const EnsPDitag dt);
EnsPDitag ensDitagNewIni(EnsPDitagadaptor dta,
ajuint identifier,
AjPStr name,
AjPStr type,
AjPStr sequence,
ajuint count);
EnsPDitag ensDitagNewRef(EnsPDitag dt);
void ensDitagDel(EnsPDitag *Pdt);
EnsPDitagadaptor ensDitagGetAdaptor(const EnsPDitag dt);
ajuint ensDitagGetCount(const EnsPDitag dt);
ajuint ensDitagGetIdentifier(const EnsPDitag dt);
AjPStr ensDitagGetName(const EnsPDitag dt);
AjPStr ensDitagGetSequence(const EnsPDitag dt);
AjPStr ensDitagGetType(const EnsPDitag dt);
AjBool ensDitagSetAdaptor(EnsPDitag dt, EnsPDitagadaptor dta);
AjBool ensDitagSetCount(EnsPDitag dt, ajuint count);
AjBool ensDitagSetIdentifier(EnsPDitag dt, ajuint identifier);
AjBool ensDitagSetName(EnsPDitag dt, AjPStr name);
AjBool ensDitagSetSequence(EnsPDitag dt, AjPStr sequence);
AjBool ensDitagSetType(EnsPDitag dt, AjPStr type);
AjBool ensDitagTrace(const EnsPDitag dt, ajuint level);
size_t ensDitagCalculateMemsize(const EnsPDitag dt);
/* Ensembl Ditag Adaptor */
EnsPDitagadaptor ensRegistryGetDitagadaptor(
EnsPDatabaseadaptor dba);
EnsPDitagadaptor ensDitagadaptorNew(EnsPDatabaseadaptor dba);
void ensDitagadaptorDel(EnsPDitagadaptor *Pdta);
EnsPBaseadaptor ensDitagadaptorGetBaseadaptor(
EnsPDitagadaptor dta);
EnsPDatabaseadaptor ensDitagadaptorGetDatabaseadaptor(
EnsPDitagadaptor dta);
AjBool ensDitagadaptorFetchAll(EnsPDitagadaptor dta,
const AjPStr name,
const AjPStr type,
AjPList dts);
AjBool ensDitagadaptorFetchAllbyIdentifiers(EnsPDitagadaptor dta,
AjPTable dts);
AjBool ensDitagadaptorFetchAllbyName(EnsPDitagadaptor dta,
const AjPStr name,
AjPList dts);
AjBool ensDitagadaptorFetchAllbyType(EnsPDitagadaptor dta,
const AjPStr type,
AjPList dts);
AjBool ensDitagadaptorFetchByIdentifier(EnsPDitagadaptor dta,
ajuint identifier,
EnsPDitag *Pdt);
/* Ensembl Ditag Feature */
EnsPDitagfeature ensDitagfeatureNewCpy(const EnsPDitagfeature dtf);
EnsPDitagfeature ensDitagfeatureNewIni(EnsPDitagfeatureadaptor dtfa,
ajuint identifier,
EnsPFeature feature,
EnsPDitag dt,
AjPStr cigar,
EnsEDitagfeatureSide side,
ajint tstart,
ajint tend,
ajint tstrand,
ajuint pairid);
EnsPDitagfeature ensDitagfeatureNewRef(EnsPDitagfeature dtf);
void ensDitagfeatureDel(EnsPDitagfeature *Pdtf);
EnsPDitagfeatureadaptor ensDitagfeatureGetAdaptor(const EnsPDitagfeature dtf);
AjPStr ensDitagfeatureGetCigar(const EnsPDitagfeature dtf);
EnsPDitag ensDitagfeatureGetDitag(const EnsPDitagfeature dtf);
EnsPFeature ensDitagfeatureGetFeature(const EnsPDitagfeature dtf);
ajuint ensDitagfeatureGetIdentifier(const EnsPDitagfeature dtf);
ajuint ensDitagfeatureGetPairidentifier(const EnsPDitagfeature dtf);
EnsEDitagfeatureSide ensDitagfeatureGetSide(const EnsPDitagfeature dtf);
ajint ensDitagfeatureGetTargetEnd(const EnsPDitagfeature dtf);
ajint ensDitagfeatureGetTargetStart(const EnsPDitagfeature dtf);
ajint ensDitagfeatureGetTargetStrand(const EnsPDitagfeature dtf);
AjBool ensDitagfeatureSetAdaptor(EnsPDitagfeature dtf,
EnsPDitagfeatureadaptor dtfa);
AjBool ensDitagfeatureSetIdentifier(EnsPDitagfeature dtf, ajuint identifier);
AjBool ensDitagfeatureSetFeature(EnsPDitagfeature dtf, EnsPFeature feature);
AjBool ensDitagfeatureSetDitag(EnsPDitagfeature dtf, EnsPDitag dt);
AjBool ensDitagfeatureSetCigar(EnsPDitagfeature dtf, AjPStr cigar);
AjBool ensDitagfeatureSetSide(EnsPDitagfeature dtf, EnsEDitagfeatureSide side);
AjBool ensDitagfeatureSetTargetStart(EnsPDitagfeature dtf, ajint tstart);
AjBool ensDitagfeatureSetTargetEnd(EnsPDitagfeature dtf, ajint tend);
AjBool ensDitagfeatureSetTargetStrand(EnsPDitagfeature dtf, ajint tstrand);
AjBool ensDitagfeatureSetPairidentifier(EnsPDitagfeature dtf, ajuint pairid);
AjBool ensDitagfeatureTrace(const EnsPDitagfeature dtf, ajuint level);
size_t ensDitagfeatureCalculateMemsize(const EnsPDitagfeature dtf);
EnsEDitagfeatureSide ensDitagfeatureSideFromStr(const AjPStr side);
const char *ensDitagfeatureSideToChar(const EnsEDitagfeatureSide dtfs);
/* AJAX List of Ensembl Ditag Feature objects */
AjBool ensListDitagfeatureSortEndAscending(AjPList dtfs);
AjBool ensListDitagfeatureSortEndDescending(AjPList dtfs);
AjBool ensListDitagfeatureSortIdentifierAscending(AjPList dtfs);
AjBool ensListDitagfeatureSortStartAscending(AjPList dtfs);
AjBool ensListDitagfeatureSortStartDescending(AjPList dtfs);
/* Ensembl Ditag Feature Adaptor */
EnsPDitagfeatureadaptor ensRegistryGetDitagfeatureadaptor(
EnsPDatabaseadaptor dba);
EnsPDitagfeatureadaptor ensDitagfeatureadaptorNew(
EnsPDatabaseadaptor dba);
void ensDitagfeatureadaptorDel(EnsPDitagfeatureadaptor *Pdtfa);
EnsPBaseadaptor ensDitagfeatureadaptorGetBaseadaptor(
EnsPDitagfeatureadaptor dtfa);
EnsPDatabaseadaptor ensDitagfeatureadaptorGetDatabaseadaptor(
EnsPDitagfeatureadaptor dtfa);
EnsPFeatureadaptor ensDitagfeatureadaptorGetFeatureadaptor(
EnsPDitagfeatureadaptor dtfa);
AjBool ensDitagfeatureadaptorFetchAllbyDitag(
EnsPDitagfeatureadaptor dtfa,
const EnsPDitag dt,
AjPList dtfs);
AjBool ensDitagfeatureadaptorFetchAllbySlice(
EnsPDitagfeatureadaptor dtfa,
EnsPSlice slice,
const AjPStr type,
const AjPStr anname,
AjPList dtfs);
AjBool ensDitagfeatureadaptorFetchAllbyType(
EnsPDitagfeatureadaptor dtfa,
const AjPStr type,
AjPList dtfs);
AjBool ensDitagfeatureadaptorFetchByIdentifier(
EnsPDitagfeatureadaptor dtfa,
ajuint identifier,
EnsPDitagfeature *Pdtf);
AjBool ensDitagfeatureadaptorRetrieveAllIdentifiers(
EnsPDitagfeatureadaptor dtfa,
AjPList identifiers);
/*
** End of prototype definitions
*/
AJ_END_DECLS
#endif /* !ENSDITAG_H */
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