/* $Id: bz_table.h,v 1.13 2003/05/14 03:05:22 schwartz Exp $ */#include "int_types.h"#include <assert.h>#ifndef ZFREE#define ZFREE(p) /*CONSTCOND*/do{ckfree(p);(p)=0;}while(0)#endiftypedef u32_t blast_ecode_t;enum { BLAST_POS_TAB_SIZE = 65536UL };  /* 65536 = 4**8 */typedef struct blast_table_w {        int W;        int num;        const signed char *encoding;        struct blast_epos_node **epos_tab;} blast_table_w;typedef struct blast_table_n {        struct hashpos **hashtab; /* array of pointers to positions in seq1, indexed by 12-mer */        struct hashpos *pool;     /* pool of free nodes */        int npool;      /* number of nodes available */        int n_node;     /* index of next free node in pool */} blast_table_n;typedef union { struct blast_table_w w; struct blast_table_n n;} blast_table_t;#ifndef SCORE_T#define SCORE_T long#endiftypedef SCORE_T score_t;typedef struct {	int len, pos1, pos2;	score_t score, cum_score;	int filter;} msp_t;typedef struct msp_table {	int size;	int num;	msp_t *msp;} msp_table_t;#define MSP_TAB_FIRST(t) ((t)->msp)#define MSP_TAB_NEXT(m) ((m)+1)#define MSP_TAB_NUM(t) ((t)->num)#define MSP_TAB_MORE(t,m) ((m-MSP_TAB_FIRST(t))<MSP_TAB_NUM(t))#define MSP_TAB_NTH(t,n) ((t)->msp[n])typedef int (*msp_cmp_t)(const void *, const void *);blast_table_t *blast_table_new(SEQ *, int);msp_table_t *blast_search(SEQ *seq1, SEQ *seq2, blast_table_t *bt, msp_table_t *mt, ss_t ss, int X, int K, int P, int T);void blast_table_free(blast_table_t *bt);void msp_free_table(msp_table_t *mt);msp_table_t *msp_new_table(void);msp_table_t *msp_compress(msp_table_t *mt);msp_table_t *msp_sort_pos1(msp_table_t *mt);msp_table_t *msp_sort(msp_table_t *mt);int msp_add(msp_table_t *, int, int, int, score_t, int);typedef int (*connect_t) (msp_t *, msp_t *, int);int msp_make_chain (msp_table_t *, int, int, int, connect_t);struct comb;int msp_extend_hit(msp_table_t *mt,                        SEQ *s1, SEQ *s2, ss_t ss, int X, int K, int W, int P,                        int pos1, int pos2,                        struct comb *diag_lev                        );