2 /* global definitions shared by dropnfa.c and altivec.c */
10 struct dstruct /* diagonal structure for saving current run */
12 int score; /* hash score of current match */
13 int start; /* start of current match */
14 int stop; /* end of current match */
15 struct savestr *dmax; /* location in vmax[] where best score data saved */
20 int score; /* pam score with segment optimization */
21 int score0; /* pam score of best single segment */
22 int gscore; /* score from global match */
23 int dp; /* diagonal of match */
24 int start; /* start of match in lib seq */
25 int stop; /* end of match in lib seq */
28 struct bdstr { int CC, DD, CP, DP;};
32 struct savestr vmax[MAXSAV]; /* best matches saved for one sequence */
33 struct savestr *vptr[MAXSAV];
34 struct savestr *lowmax;
37 int hmask; /* hash constants */
38 int *pamh1; /* pam based array */
39 int *pamh2; /* pam based kfact array */
40 int *link, *harr; /* hash arrays */
41 int kshft; /* shift width */
42 int nsav, lowscor; /* number of saved runs, worst saved run */
49 struct swstr *f_ss, *r_ss;
60 vector signed ALTIVEC_SIZE *vec_HH;
61 vector signed ALTIVEC_SIZE *vec_EE;
64 vecInt2 **vec_matrix2;
65 vector signed ALTIVEC_SIZE2 *vec_HH2;
66 vector signed ALTIVEC_SIZE2 *vec_EE2;
71 FLOCAL_ALIGN(const unsigned char *A, const unsigned char *B,
72 int M, int N, int low, int up,
73 int **W, int G,int H, int MW,
74 struct f_struct *f_str);