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/* @include enstranslation ****************************************************
**
** Ensembl Translation functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.30 $
** @modified 2009 by Alan Bleasby for incorporation into EMBOSS core
** @modified $Date: 2013/02/17 13:10:30 $ 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 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);
EnsPBaseadaptor ensTranslationadaptorGetBaseadaptor(
EnsPTranslationadaptor tla);
EnsPDatabaseadaptor ensTranslationadaptorGetDatabaseadaptor(
EnsPTranslationadaptor tla);
AjBool ensTranslationadaptorFetchAllbyExternaldatabasename(
EnsPTranslationadaptor tla,
const AjPStr dbname,
AjPList translations);
AjBool ensTranslationadaptorFetchAllbyExternalname(
EnsPTranslationadaptor tla,
const AjPStr name,
const AjPStr dbname,
AjBool override,
AjPList translations);
AjBool ensTranslationadaptorFetchAllbyIdentifiers(
EnsPTranslationadaptor tla,
AjPTable 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 stableids);
/*
** End of prototype definitions
*/
AJ_END_DECLS
#endif /* !ENSTRANSLATION_H */
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