2 /* $Name: fa_34_26_5 $ - $Id: structs.h,v 1.36 2006/06/22 02:35:05 wrp Exp $ */
4 #include "aln_structs.h"
9 int histint, min_hist, max_hist, maxh;
12 char stat_info[MAX_STR];
21 struct mngmsg /* Message from host to manager */
23 int n0; /* Integer returned by hgetseq */
24 int nm0; /* number of segments */
25 int nmoff; /* length of fastf segment */
26 unsigned char *aa0a; /* annotation array */
27 char ann_arr[MAX_FN]; /* annotation characters */
28 int ann_flg; /* have annotation array, characters */
29 char tname[MAX_FN]; /* Query sequence name */
30 int tnamesize; /* Query name size */
35 char lname[MAX_FN]; /* Library file name */
36 char *lbnames[MAX_LF]; /* list of library files */
37 struct lmf_str *lb_mfd[MAX_LF]; /* list of opened file pointers */
39 int max_tot; /* function defined total sequence area */
40 int maxn; /* longest library sequence chunk */
41 int dupn; /* overlap to use when segmenting sequence (p_comp) */
42 int qoff; /* overlap when segmenting long query sequence */
43 int loff; /* overlap when segmenting long library sequences */
44 int maxt3; /* overlap for tranlated sequences */
45 int qdnaseq; /* query is protein (0)/dna (1) */
46 int ldnaseq; /* library is protein (0)/dna (1) */
47 int qframe; /* number of possible query frames */
48 int nframe; /* frame for TFASTA */
49 int nitt1; /* nframe-1 */
50 int thr_fact; /* fudge factor for threads */
51 int s_int; /* sampling interval for statistics */
52 int ql_start; /* starting query sequence */
53 int ql_stop; /* ending query sequence */
54 int nln; /* number of library names */
55 int pbuf_siz; /* buffer size for sequences send in p2_complib */
56 char qtitle[MAX_FN]; /* query title */
57 char ltitle[MAX_FN]; /* library title */
58 char flstr[MAX_FN]; /* FASTLIBS string */
60 char label [MAXLN]; /* Output label */
61 char f_id0[4]; /* function id for markx==10 */
62 char f_id1[4]; /* function id for markx==10 */
63 char sqnam[4]; /* "aa" or "nt" */
64 char sqtype[10]; /* "DNA" or "protein" */
65 int long_info; /* long description flag*/
66 long sq0off, sq1off; /* offset into aa0, aa1 */
67 int markx; /* alignment display type */
68 int seqnm; /* query sequence number */
69 int nbr_seq; /* number of library sequences */
70 int term_code; /* add termination codes to proteins if absent */
71 int n1_high; /* upper limit on sequence length */
72 int n1_low; /* lower limit on sequence length */
73 double e_cut; /* e_value for display */
74 double e_low; /* e_value for display */
75 int e_cut_set; /* e_value deliberately set */
76 int pamd1; /* 1st dimension of pam matrix */
77 int pamd2; /* 2nd dimension of pam matrix */
78 int revcomp; /* flag to do reverse complement */
79 int quiet; /* quiet option */
80 int nrelv; /* number of interesting scores */
81 int srelv; /* number of scores to show in showbest */
82 int arelv; /* number of scores to show at alignment */
83 int z_bits; /* z_bits==1: show bit score, ==0 show z-score */
84 char alab[3][24]; /* labels for alignment scores */
85 int nohist; /* no histogram option */
87 int mshow; /* number of scores to show */
89 int ashow; /* number of alignments to show */
90 int nmlen; /* length of name label */
91 int show_code; /* show alignment code in -m 9; ==1 => identity only, ==2 alignment code*/
92 int self; /* self comparison */
93 int thold; /* threshold */
94 int last_calc_flg; /* needs a last calculation stage */
95 int qshuffle; /* shuffle the query and do additional comparisons */
96 int shuff_max; /* number of shuffles to perform */
97 int shuff_node; /* number of shuffles/worker node */
99 int stages; /* number of stages */
100 double Lambda, K, H; /* Karlin-Altschul parameters */
101 int escore_flg; /* use escore calculated by do_work() */
102 struct hist_str hist;
105 struct a_struct aln; /* has llen, llnctx, llnctx_flg, showall */
106 struct a_res_str a_res; /* has individual alignment coordinates */
107 char dfile [MAX_FN]; /* file for dumping scores to */