3 /* $Name: fa_34_26_5 $ - $Id: drop_func.h,v 1.7 2006/05/31 15:31:45 wrp Exp $ */
5 /* functions provided by each of the drop files */
7 /* Copyright (c) 2005 William R. Pearson and the University of Virginia */
10 void /* initializes f_struct **f_arg */
11 init_work (unsigned char *aa0, int n0,
16 struct f_struct **f_arg
21 void /* frees memory allocated in f_struct */
22 close_work (const unsigned char *aa0, int n0,
27 struct f_struct **f_arg
31 void /* documents search function, parameters */
32 get_param (struct pstruct *pstr, char *pstring1, char *pstring2);
34 void /* calculates alignment score(s), returns them in rst */
35 do_work (const unsigned char *aa0, int n0,
36 const unsigned char *aa1, int n1,
42 struct f_struct *f_arg,
44 int qr_flg, struct rstruct *rst);
46 void /* calculates optimal alignment score */
47 do_opt (const unsigned char *aa0, int n0,
48 const unsigned char *aa1, int n1,
54 struct f_struct *f_arg,
59 int /* produces encoding of alignment */
60 do_walign (const unsigned char *aa0, int n0,
61 const unsigned char *aa1, int n1,
67 struct f_struct *f_arg,
69 struct a_res_str *a_res,
73 pre_cons(const unsigned char *aa, int n, int frame,
77 struct f_struct *f_arg
82 aln_func_vals(int frame, struct a_struct *aln);
84 int /* takes aa0, aa1, a_res, and produces seqc0, seqc1 */
85 calcons(const unsigned char *aa0, int n0,
86 const unsigned char *aa1, int n1,
88 struct a_struct *aln, /* seqc0/seqc1 coordinates */
89 struct a_res_str a_res, /* aa0,aa1, coord, inc. res, nres */
91 char *seqc0, char *seqc1, char *seqca,
95 struct f_struct *f_arg
99 /* calcons_a - takes aa0, aa1, a_res, and produces seqc0, seqc1,
100 * and seqc0a, seqc1a - the annotated sequences
103 calcons_a(const unsigned char *aa0, unsigned char *aa0a, int n0,
104 const unsigned char *aa1, int n1,
106 struct a_struct *aln,
107 struct a_res_str a_res,
109 char *seqc0, char *seqc0a, char *seqc1, char *seqca,
114 struct f_struct *f_arg
118 int /* returns lenc - length of aligment */
119 calc_code(const unsigned char *aa0, int n0,
120 const unsigned char *aa1, int n1,
121 struct a_struct *aln,
122 struct a_res_str a_res,
124 char *al_str, int al_str_n,
128 struct f_struct *f_arg
132 int /* returns lenc - length of alignment */
133 calc_id(const unsigned char *aa0, int n0,
134 const unsigned char *aa1, int n1,
135 struct a_struct *aln,
136 struct a_res_str a_res,
141 struct f_struct *f_arg