1 /* $Name: fa_34_26_5 $ - $Id: param.h,v 1.41 2007/04/26 18:37:19 wrp Exp $ */
10 /* Concurrent read version */
37 struct pstruct /* parameters */
39 int n0; /* length of query sequence, used for statistics */
40 int gdelval; /* value gap open (-10) */
41 int ggapval; /* value for additional residues in gap (-2) */
42 int gshift; /* frameshift for fastx, fasty */
43 int gsubs; /* nt substitution in fasty */
44 int p_d_mat; /* dna match penalty */
45 int p_d_mis; /* dna mismatch penalty */
46 int p_d_set; /* using match/mismatch */
47 int score_ix; /* index to sorted score */
48 int zsflag; /* use scalebest() */
49 int zsflag_f; /* use scalebest() */
51 int histint; /* histogram interval */
54 int nsq; /* length of normal sq */
55 int ext_sq_set; /* flag for using extended alphabet */
59 int nsqx; /* length of extended sq */
60 int dnaseq; /* -1 = not set (protein); 0 = protein; 1 = DNA; 2 = other, 3 RNA */
61 int nt_align; /* DNA/RNA alignment = 1 */
63 int tr_type; /* codon table */
65 char pamfile[120]; /* pam file type */
74 int pamoff; /* offset for pam values */
75 int pam_l, pam_h, pam_xx, pam_xm; /* lowest, highest pam value */
77 int pam_ms; /* use a Mass Spec pam matrix */
79 long zdb_size; /* force database size */
89 /* Result structure - do not remove */
106 struct pstruct *ppst;
114 #include <sys/types.h>
116 /* this structure passes library sequences to the worker threads
117 and returns scores */
128 struct lmf_str *m_file_p;
134 char libstr[20]; /* set to MAX_UID */
136 int r_score, qr_score;
137 double r_escore, qr_escore;
143 unsigned char *start;
151 #include "aln_structs.h"