/*  File: aligntools.h
 *  Author: Ulrich Sauvage (ulrich@kaa.crbm.cnrs-mop.fr)
 *  Copyright (C) J Thierry-Mieg and R Durbin, 1994
 * -------------------------------------------------------------------
 * 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 (MRC LMB, UK) rd@mrc-lmba.cam.ac.uk, and
 *	Jean Thierry-Mieg (CRBM du CNRS, France) mieg@kaa.cnrs-mop.fr
 *
 * Description:
 * Exported functions:
 * HISTORY:
 * Last edited: Mar  6 17:12 1996 (srk)
 * Created: Thu Jun  2 13:22:15 1994 (ulrich)
 *-------------------------------------------------------------------
 */

/*  $Id: aligntools.h,v 1.14 1999/09/01 11:03:14 fw Exp $ */

#ifndef DEFINE_ALIGNTOOLS_h
#define DEFINE_ALIGNTOOLS_h

#define OVERLAP_MIN 20 /* overlap minimum entre 2 dna successifs */
#define NB_OCTET 3 /* dodecameres sur 3 octets */
#define DODECA 12 /* taille des oligos */
#define GO_AFT_ERREUR 5
#define GO_AFT_SINGLE 4
#define GO_AFT_DOUBLE 7
static unsigned int mask = 1 << 24 ; /* pour avoir des dodecameres */

unsigned int dnaComplement(unsigned int lambda, int noct) ;
Array monDnaGet (DEFCPT look, KEY contig, KEY key) ;
void monDnaInsert(DEFCPT look, KEY key, Array dna) ;
void monDnaForget(DEFCPT look, KEY key) ;
/* void monDnaRemove (DEFCPT look) ; */

BOOL alignToolsMakeOligo(Array dna, int debut, int fin, int taille, 
			 unsigned int *oligo, int *pos) ;
Array alignToolsFindShortOligo(Array dna, int xd, int xf, 
				      unsigned int win, int taille,
				      unsigned int olig) ;
void alignToolsMakeSuccesOligo (Array dna, Associator oligo, int x1, 
				int x2, int taille) ;
void alignToolsFindColorOligo (Array dna, Associator oligo, Array color,
			       int taille) ;
void alignToolsInit (void) ;
void alignToolsDestroy (DEFCPT look) ;
Array alignToolsMatch(Array longDna, int xmin, int xmax, int x1, int x2,
		      Array shortDna, int ymin, int ymax, int y1, int y2,
		      int *debut, int *fin, int *sens, int all, int taux, 
		      int nbessai, BOOL control) ;
/*void doForceAssembleSeg(KEY seg, KEY target, int let, int cut) ;*/
void doForceAssembleSeg (DEFCPT look, KEY seg, KEY target, int min, int max,
			 int let, int cut) ;
Array alignToolsCptErreur(Array longDna, Array shortDna, int *debutp, int *finp,
			  int *shdebutp, int *shfinp) ;
Array alignToolsMakeErreur(Array longDna, int *debutp, int *finp, int pols, 
			   Array shortDna, int shdeb, int shfin, int pos, int sens) ;
void localCptErreur(Array longDna, int xl1, int xl2, int pol,
		    Array shortDna, int xs1, int xs2, int pos, int sens,
		    int *nbN, int *start, int *stop, int *recouv, Array errArray) ;

void alignToolsCheckArray (Array units, int width, int decal, int sens) ;

#endif