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#ifndef _MCONSIST_
#define _MCONSIST_
#include <sequtil.h>
#include <objalign.h>
#undef NLM_EXTERN
#ifdef NLM_IMPORT
#define NLM_EXTERN NLM_IMPORT
#else
#define NLM_EXTERN extern
#endif
/****************************************************************************
*
* get_anchor_coordinates(h_align, anchor_id, sip, x_anchor_pos, x_pos, num)
*
* load the positions of framework marker of the current sequence and its
* corresponding positions in the anchor map (normally the NCBI sequence) into
* two arays to extrapolate the positions for map integration
* h_align: the alignment of consistent markers (a.k.a good alignment)
* anchor_id: the Seq-id for the anchor map (normally, the NCBI sequence map)
* sip: the Seq-id for the current sequence
* x_anchor_pos: the array to store the positions on the anchor map
* x_pos: the array to store the positions on the current map. each
* member of x_anchor_pos and x_pos is a matching pair
* both arrays are ordered
* num: the total number of framework markers in the current map.
* This is also the size of x_anchor_pos and x_pos
*
* return TRUE for success and FALSE for fail
*
****************************************************************************/
NLM_EXTERN Boolean get_anchor_coordinates PROTO((SeqAlignPtr h_align, SeqIdPtr anchor_id, SeqIdPtr sip, Int4Ptr PNTR x_anchor_pos, Int4Ptr PNTR x_pos, Uint2Ptr num));
/****************************************************************************
*
* find_this_position_by_anchor(anchor_pos, pos, num, this_pos, length)
* map the position on the current map to the anchor map (sequence map)
* anchor_pos, pos: the two arrays of matching positions on the anchor mark
* and the current map for the consistent markers
* num: number of the consistent markers on the current map. (same as the
* size of the anchor marker)
* this_pos: the position on the current map
* length: the length of the anchor map
*
* return the position mapped to the anchor marker
*
*****************************************************************************/
NLM_EXTERN Int4 find_this_position_by_anchor PROTO((Int4Ptr anchor_pos, Int4Ptr pos, Uint2 num, Int4 this_pos, Int4 length));
NLM_EXTERN Boolean find_flanking_anchor_pos PROTO((Int4Ptr anchor_pos, Uint2 num, Int4 c_pos, Int4 length, Int4Ptr f_left, Int4Ptr f_right));
/**********************************************************************
*
* MapLocToAnchor(annot, slp, anchor)
* map the current slp to a position on the anchor Bioseq
* annot: Seq-annot that may contain the alignment of the consistent markers
* slp: the current Bioseq
* anchor_id: the Seq-id for the anchor Bioseq, that is the sequece map
*
************************************************************************/
NLM_EXTERN SeqLocPtr MapLocToAnchor PROTO((SeqAnnotPtr annot, SeqLocPtr slp, BioseqPtr anchor_bsp));
/*****************************************************************
*
* map a position on the anchor_bsp (anchor_pos) to a
* position on the other_bsp. It is the reverse operation of
* MapLocToAnchor
* return -1 for failure
*
******************************************************************/
NLM_EXTERN Int4 MapAnchorToLoc PROTO((SeqAnnotPtr annot, Int4 anchor_pos, BioseqPtr anchor_bsp, BioseqPtr other_bsp));
#undef NLM_EXTERN
#ifdef NLM_EXPORT
#define NLM_EXTERN NLM_EXPORT
#else
#define NLM_EXTERN
#endif
#endif
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