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/* @include ensintron *********************************************************
**
** Ensembl Intron functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.13 $
** @modified 2009 by Alan Bleasby for incorporation into EMBOSS core
** @modified $Date: 2013/02/17 13:07:53 $ 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 ENSINTRON_H
#define ENSINTRON_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ensdata.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
/* Ensembl Intron */
EnsPIntron ensIntronNewCpy(const EnsPIntron intron);
EnsPIntron ensIntronNewIni(EnsPExon exon1,
EnsPExon exon2,
EnsPAnalysis analysis);
EnsPIntron ensIntronNewRef(EnsPIntron intron);
void ensIntronDel(EnsPIntron *Pintron);
EnsPFeature ensIntronGetFeature(const EnsPIntron intron);
EnsPExon ensIntronGetNextexon(const EnsPIntron intron);
EnsPExon ensIntronGetPreviousexon(const EnsPIntron intron);
AjBool ensIntronSetFeature(EnsPIntron intron,
EnsPFeature feature);
AjBool ensIntronSetNextexon(EnsPIntron intron,
EnsPExon exon);
AjBool ensIntronSetPreviousexon(EnsPIntron intron,
EnsPExon exon);
AjBool ensIntronTrace(const EnsPIntron intron, ajuint level);
ajuint ensIntronCalculateLength(const EnsPIntron intron);
size_t ensIntronCalculateMemsize(const EnsPIntron intron);
AjBool ensIntronFetchSplicesequences(const EnsPIntron intron,
AjPStr *Pdonor,
AjPStr *Pacceptor);
AjBool ensIntronIsCanonical(const EnsPIntron intron, AjBool *Presult);
AjBool ensIntronMatch(const EnsPIntron intron1,
const EnsPIntron intron2);
EnsPIntron ensIntronTransfer(EnsPIntron intron,
EnsPSlice slice);
EnsPIntron ensIntronTransform(EnsPIntron intron,
const AjPStr csname,
const AjPStr csversion);
/* Ensembl Intron Supporting Evidence */
EnsPIntronsupportingevidence ensIntronsupportingevidenceNewCpy(
const EnsPIntronsupportingevidence ise);
EnsPIntronsupportingevidence ensIntronsupportingevidenceNewIni(
EnsPIntronsupportingevidenceadaptor isea,
ajuint identifier,
EnsPFeature feature,
EnsPIntron intron,
AjPStr hitname,
AjBool canonical,
double score,
EnsEIntronsupportingevidenceType type);
EnsPIntronsupportingevidence ensIntronsupportingevidenceNewRef(
EnsPIntronsupportingevidence ise);
void ensIntronsupportingevidenceDel(EnsPIntronsupportingevidence *Pise);
EnsPIntronsupportingevidenceadaptor ensIntronsupportingevidenceGetAdaptor(
const EnsPIntronsupportingevidence ise);
AjBool ensIntronsupportingevidenceGetCanonical(
const EnsPIntronsupportingevidence ise);
EnsPFeature ensIntronsupportingevidenceGetFeature(
const EnsPIntronsupportingevidence ise);
AjPStr ensIntronsupportingevidenceGetHitname(
const EnsPIntronsupportingevidence ise);
ajuint ensIntronsupportingevidenceGetIdentifier(
const EnsPIntronsupportingevidence ise);
EnsPIntron ensIntronsupportingevidenceGetIntron(
const EnsPIntronsupportingevidence ise);
double ensIntronsupportingevidenceGetScore(
const EnsPIntronsupportingevidence ise);
EnsEIntronsupportingevidenceType ensIntronsupportingevidenceGetType(
const EnsPIntronsupportingevidence ise);
AjBool ensIntronsupportingevidenceSetFeature(
EnsPIntronsupportingevidence ise,
EnsPFeature feature);
AjBool ensIntronsupportingevidenceTrace(
const EnsPIntronsupportingevidence ise,
ajuint level);
size_t ensIntronsupportingevidenceCalculateMemsize(
const EnsPIntronsupportingevidence ise);
AjBool ensIntronsupportingevidenceFetchExons(
const EnsPIntronsupportingevidence ise,
EnsPTranscript transcript,
EnsPExon *Previous,
EnsPExon *Pnext);
AjBool ensIntronsupportingevidenceMatch(
const EnsPIntronsupportingevidence ise1,
const EnsPIntronsupportingevidence ise2);
EnsPIntronsupportingevidence ensIntronsupportingevidenceTransfer(
EnsPIntronsupportingevidence ise,
EnsPSlice slice);
EnsPIntronsupportingevidence ensIntronsupportingevidenceTransform(
EnsPIntronsupportingevidence ise,
const AjPStr csname,
const AjPStr csversion);
AjBool ensIntronsupportingevidenceHasTranscripts(
const EnsPIntronsupportingevidence ise,
AjBool *Presult);
EnsEIntronsupportingevidenceType ensIntronsupportingevidenceTypeFromStr(
const AjPStr type);
const char* ensIntronsupportingevidenceTypeToChar(
EnsEIntronsupportingevidenceType iset);
/* Ensembl Intron Supporting Evidence Adaptor */
EnsPIntronsupportingevidenceadaptor ensRegistryGetIntronsupportingevidenceadaptor(
EnsPDatabaseadaptor dba);
EnsPIntronsupportingevidenceadaptor ensIntronsupportingevidenceadaptorNew(
EnsPDatabaseadaptor dba);
void ensIntronsupportingevidenceadaptorDel(
EnsPIntronsupportingevidenceadaptor *Pisea);
EnsPBaseadaptor ensIntronsupportingevidenceadaptorGetBaseadaptor(
EnsPIntronsupportingevidenceadaptor isea);
EnsPDatabaseadaptor ensIntronsupportingevidenceadaptorGetDatabaseadaptor(
EnsPIntronsupportingevidenceadaptor isea);
EnsPFeatureadaptor ensIntronsupportingevidenceadaptorGetFeatureadaptor(
EnsPIntronsupportingevidenceadaptor isea);
AjBool ensIntronsupportingevidenceadaptorFetchAllbyTranscript(
EnsPIntronsupportingevidenceadaptor isea,
const EnsPTranscript transcript,
AjPList ises);
AjBool ensIntronsupportingevidenceadaptorFetchByIdentifier(
EnsPIntronsupportingevidenceadaptor isea,
ajuint identifier,
EnsPIntronsupportingevidence *Pise);
AjBool ensIntronsupportingevidenceadaptorRetrieveExonidentifiers(
EnsPIntronsupportingevidenceadaptor isea,
const EnsPIntronsupportingevidence ise,
const EnsPTranscript transcript,
ajuint *Previous,
ajuint *Pnext);
AjBool ensIntronsupportingevidenceadaptorRetrieveAllTranscriptidentifiers(
EnsPIntronsupportingevidenceadaptor isea,
const EnsPIntronsupportingevidence ise,
AjPList transcriptids);
/*
** End of prototype definitions
*/
AJ_END_DECLS
#endif /* !ENSINTRON_H */
|
