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/* File: cdna.h
* Author: mieg
* Copyright (c) J Thierry-Mieg and R Durbin, 1999
* -------------------------------------------------------------------
* Acedb is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
* or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
* -------------------------------------------------------------------
* This file is part of the ACEDB genome database package, written by
* Richard Durbin (Sanger Centre, UK) rd@sanger.ac.uk, and
* Jean Thierry-Mieg (CRBM du CNRS, France) mieg@kaa.crbm.cnrs-mop.fr
*
* Description:
* Exported functions:
* HISTORY:
* Last edited: Nov 15 15:54 1999 (fw)
* Created: Thu Aug 26 17:55:00 1999 (fw)
* CVS info: $Id: cdna.h,v 1.11 2000/04/14 21:47:04 mieg Exp $
*-------------------------------------------------------------------
*/
#ifndef ACEDB_CDNA_H
#define ACEDB_CDNA_H
#include "acedb.h"
#include "whooks/sysclass.h"
extern Array fMapcDNAReferenceDna ;
extern Array fMapcDNAReferenceHits ;
extern KEY fMapcDNAReferenceGene ;
extern KEY fMapcDNAReferenceEst ;
extern int fMapcDNAReferenceOrigin ;
Array cDNAGetReferenceHits (KEY gene, int origin) ;
KEY cDNARealignGene (KEY gene, int z1, int z2) ;
void fMapcDNADoSelect(KEY k, KEYSET ks, KEYSET taceKs) ;
KEY cDNAMakeDna (KEY gene) ;
typedef struct hitStruct { KEY gene, cDNA_clone, est ; BOOL reverse ;
int a1, a2, x1, x2, clipTop, clipEnd ; int type, zone ; Array errArray ; } HIT ;
extern char B2[255] ;
extern KEY
_VTranscribed_gene, _Transcribed_gene,
_VTranscript, _Transcript,
_VAnnotation,
_VcDNA_clone, _VSage, _Sage,
_VClone_Group , _Clone_Group, _From_gene,
_cDNA_clone, _Hit , _Forward, _Reverse,
_Confirmed_intron , _Confirmed_exon,
_First_exon, _Last_exon,
_Splicing, _Read,
_Nb_possible_exons, _Nb_alternative_exons,
_Nb_confirmed_introns, _Nb_confirmed_alternative_introns,
_Intron, _Exon, _Gap,
_Alternative_exon, _Alternative_first_exon, _Alternative_intron,
_Partial_exon, _Alternative_partial_exon,
_3prime_UTR, _5prime_UTR,
_Begin_not_found, /* _End_not_found, */
_Total_length, _Total_intron_length, _Total_gap_length,
_Transpliced_to, _Transcribed_from, _Genomic_sequence,
_PolyA_after_base, _Intron_boundaries,
_Fake_internal_poly_A, _Vector_clipping, _Reversed_by, _Other,
_Read_matchingLength_nerrors, _PCR_product_size, _Primed_on_polyA,
_Assembled_from_cDNA_clone, _Genomic_sequence,
_Spliced_sequence, _From_gene, _NewName, _3prime_UTR_length, _Longest_cDNA_clone,
_Overlap_right, _Overlap_left, _Is_chain, _Is_gap, _Genomic,
_IntMap, _Hits, _Mosaic, _Problem, _Gene_wall, _Relabelled,
_Discarded_cDNA, _Discarded_from,
_Derived_sequence,
_CTF_File ;
void cDNAAlignInit (void) ;
void cDNARemoveCloneFromGene (KEY clone, KEY gene); /* cdnaalign.c */
#endif /* !ACEDB_CDNA_H */
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