#ifndef BZ_MAIN_H#define BZ_MAIN_H#include "bz_all.h"void *ckrealloc(void *, size_t);typedef struct bz_flags {    int C, G, H, K, L, M, P, R, T, W, X, Y;} bz_flags_t;typedef struct tback {	uchar *space;		/* array to be used. */	unsigned int len;	/* length of that array. */} TB, *TBack;typedef struct align_ {        int beg1, beg2, end1, end2;        struct align_ *next_align;        edit_script_t *script;	int score;	uchar *seq1, *seq2;} align_t;uchar *reverse_seq(uchar *s, int len);align_t *bz_extend_msps(SEQ *, uchar *, SEQ *, msp_table_t *, gap_scores_t *, ss_t,  int, int, TBack);/* ----------------- end of header information used by blastz.c ------------- *//* ----------- what follows is shared by bz_extend.c and bz_align.c ----------*//* block types: */#define DIA 0#define HOR 1#define VER 2/* Alignment segments */typedef struct bl {	int b1, b2, e1, e2;	char type;	struct bl *next_block, *prev_block;} block, *block_ptr;/* Expanded structure for each MSP */typedef struct msp1 {	int	  pos1, pos2,	/* initially, midpoints of best 31-mer, .. */			/* then start-points of the seeded alignment */	  end1, end2;	/* end-points of alignments seeded by the MSP */	/* We keep two forms of the aligment seeded by this MSP.  The first	*  is a linked list of diagonal, horizontal and vertical segments. */	block_ptr first_block, last_block; /* is last_block needed? */	/* The second form of the alignment is for external consumption. */	align_t *align;	/* At the alignment's beginning and ending points, we keep pointers	*  to the alignments and alignment blocks immediately above and below	*  the terminus. */	struct msp1 *up_align1, *down_align1, *up_align2, *down_align2;	block_ptr up_block1, down_block1, up_block2, down_block2;	/* Alignments are linked both by increasing start-point and by	*  decreasing end-point. */	struct msp1 *next_msp, *prev_msp;} Msp_node, *Msp_ptr;/* Structure holding input and output for Align().  */typedef struct _gapalign_blk {	/* The following must be supplied by caller.  */	uchar 	*seq1,		/* the query sequence. */		*seq2,		/* the subject sequence. */		*seq1_r,	/* reverse of query */		*seq2_r;  	/* reverse of subject*/	int	len1,		/* the length of the query. */		len2,		/* the subject length. */		seed1,		/* query position to start the alignment. */		seed2,		/* subject position to start the alignment.*/ 		gap_open,	/* cost to open a gap. */		gap_extend,	/* cost to extend a gap. */		x_parameter;	/* values of X-dropoff parameter. */	Msp_ptr Up_align,	/* closest alignment above (right of) seed pt */		Down_align,	/* closest alignment below (left of) seed pt */		Right_list,	/* alignments starting after the seed point */		Left_list;	/* alignments ending before the seed point */	block_ptr		Up_block,	/* specific block of Up_align */		Down_block;	/* specific block of Down_align */	int	**subscore;	/* nucleotide substitution scores. */	TBack tback;		/* block of memory for alignment trace-back */	/* The following are returned by Align(). */	int	score, 		/* score of alignment. */		start1,		/* start of alignment on query. */		start2,		/* start of alignment on subject. */		stop1,		/* end of alignment on query. */		stop2;		/* end of alignment on subject. */        edit_script_t *ed_scr;	/* alignment's edit script */} AlignIO, *AlignIOPtr;void Align(AlignIOPtr);#endif /* BZ_MAIN_H */