/*  File: dotter.h
 *  Author: Erik Sonnhammer
 *  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:
 *   Only 3 parameters are mandatory, the rest can be set to NULL.
 *   A minimal call would look like:
 *
 *   dotter(type, 0, 0, qseq, 0, 0, sseq, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0);
 *
 *   NOTE: qseq and sseq must be messalloc'ed in the calling routine.  
 *   They are messfree'd by Dotter.
 *
 * HISTORY:
 * Last edited: Jan 18 11:34 2002 (edgrif)
 * Created: Thu Aug 26 17:16:19 1999 (fw)
 * CVS info:   $Id: dotter.h,v 1.22 2002/01/18 12:06:06 edgrif Exp $
 *-------------------------------------------------------------------
 */
#ifndef DEF_DOTTER_H
#define DEF_DOTTER_H

#include "blxview.h"   /* For MSP struct */

Graph 
dotter (

	char  type,        /* Mandatory, one of { P, N, X } 
			      P -> Protein-Protein
			      N -> DNA-DNA
			      X -> DNA-Protein */
	
	char *opts,        /* Optional, may be NULL 
			      Various options for display features */

	char *queryname,   /* Optional, may be NULL 
			      Name of Horizontal sequence */
	
	char *queryseq,	   /* Mandatory, NULL terminated string
			      Horisontal sequence - messfree'd by Dotter */

	int   qoff,	   /* Optional, may be NULL
			      Coordinate offset of horisontal sequence */

	char *subjectname, /* Optional, may be NULL 
			      Name of vertical sequence */

	char *subjectseq,  /* Mandatory, NULL terminated string
			      vertical sequence - messfree'd by Dotter */

	int   soff,	   /* Optional, may be NULL 
			      Coordinate offset of horisontal sequence */

	int   qcenter,	   /* Optional, may be NULL 
			      Coordinate to centre horisontal sequence on */

	int   scenter,	   /* Optional, may be NULL 
			      Coordinate to centre horisontal sequence on */

	char *savefile,	   /* Optional, may be NULL 
			      Filename to save dotplot to. Invokes batch mode */

	char *loadfile,	   /* Optional, may be NULL 
			      Filename to load dotplot from */

	char *mtxfile,	   /* Optional, may be NULL 
			      Filename to load score matrix from */

	float memoryLimit, /* Optional, may be NULL 
			      Maximum Mb allowed for dotplot */

	int   zoomFac,	   /* Optional, may be NULL
			      Compression of dotplot {1, 2, 3, ... }
			      Automatically calculated if NULL */

	MSP  *MSPlist,	   /* Optional, may be NULL
			      List of MSPs containing genes and blast matches */

	int   MSPoffset,   /* Optional, may be NULL
			      Coordinate offset of MSPs */

	char *winsize,	   /* String determining the window size */

	int   pixelFacset  /* Preset pixel factor */
);


/* Find an executable and return its complete pathname. */
int findCommand (char *command, char **retp) ;


#endif /*  !defined DEF_DOTTER_H */