/*  File: smap_.h
 *  Author: Ed Griffiths (edgrif@sanger.ac.uk)
 *  Copyright (c) Sanger Institute, 2003
 *-------------------------------------------------------------------
 * ZMap 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, originated 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: Data structs etc. internal to SMap.
 * HISTORY:
 * Last edited: Oct 31 10:03 2003 (edgrif)
 * Created: Fri Oct 31 09:45:55 2003 (edgrif)
 * CVS info:   $Id: smap_.h,v 1.1 2003/11/05 09:43:30 edgrif Exp $
 *-------------------------------------------------------------------
 */
#ifndef DEF_SMAP_P_H
#define DEF_SMAP_P_H

#include <wh/smap.h>					    /* External header. */



/********** data structures ****************************************/

typedef struct
{
  int s1, s2 ;	/* start/end of segments allowed to disagree, 
		   in source coordinates */
} SMapMismatch ;


typedef enum {strand_up, strand_down} Strand ;

#define invertStrand(x) ((x) == strand_down ? strand_up : strand_down)



/* For each key, the keyInfo record gives an array for the map and an
   array of mismatch information, which can be null. It also records the strand
   of this key relative to its parent, this is needed because otherwise we cannot
   tell the strand of features that are 1 base long. The length of this key in
   its parent is also recorded because the coordinates in the "map" array may have
   been clipped and hence cannot reliably be used for positioning of child features
   that are reversed with respect to this keys coordinates (i.e. we always know
   the key starts at "1" and hence clipping of the start does not matter, but if
   the end is clipped we have no way of knowing the length unless we record it
   separately.

   Each SMapMap structure in map defines a set of intervals in the 
   coordinate system of key, each interval being mapped as an ungapped
   block to a corresponding interval in the SMap's coordinates.
   
   Each [s1,s2] pair in mismatch defines a set of intervals in the 
   coordinate system of key that can contain mismatches to the canonical 
   sequence.

   Both ->map and ->mismatch arrays are sorted in increasing order of s1, 
   and s2 >= s1 always.  We also assume here that the sequences are 
   colinear.
*/
struct SMapKeyInfoStruct
{
  KEY key, parent ;
  Strand strand ;					    /* vital for features of length = 1 */
  int length ;						    /* Of this object in the parent. */
  SMap *smap ;
  Array map ;						    /* of SMapMap */
  Array inverseMap ;					    /* of SMapMap - filled lazily */
  Array mismatch ;					    /* of SMapMisMatch */
  Array children ;					    /* of SMapKeyInfo* */
} ;



/* This is the main structure representing an SMap, this points to all the other information
 * for an SMap. */
struct SMapStruct
{
  STORE_HANDLE handle ;		/* the SMap's own handle */
  Associator key2index ;	/* index into keyInfo */
  SMapKeyInfo *root ;
  int length ;
  int area1, area2;

  /* following is a simple cache for key2index mapping */
  SMapKeyInfo *lastKeyInfo ;

#ifdef ACEDB4
  Array lastKeyUnspliced;
#endif
} ;


/* Struct used to return result of mapping, y1 & y2 are the original coordinates remapped into
 * root coordinates. nx1 & nx2 are the original coordinates truncated to fit into the root
 * coordinate system, if no truncation was necessary then they will be original coordinates. */
struct SMapMapReturn
{
  int y1, y2; /* root co-ordinates */
  int nx1, nx2; /* truncated local co-ordinates */
};




/* Used by internal exon sorting routines. */
typedef struct { int x, y ; } ExonStruct ;




#endif /* DEF_SMAP_P_H */