2 case 'a': m_msg->aln.showall = 1;
3 case 'B': m_msg->z_bits = 0;
6 case 'd': m_msg->ashow);
7 case 'D': ppst->debug_lib = 1;
10 case 'f': ppst->gdelval
11 case 'g': ppst->ggapval
12 case 'H': m_msg->nohist = 1; break;
13 case 'i': m_msg->revcomp = 1; break;
14 case 'I': m_msg->self = 1; break;
15 case 'J': m_msg->ql_start, ql_stop
16 case 'K': max_buf_cnt (PCOMPLIB)
17 case 'l': m_msg->flstr
18 case 'L': m_msg->long_info = 1
19 case 'M': m_msg->n1_low,&m_msg->n1_high
20 case 'm': m_msg->markx
21 case 'n': m_msg->qdnaseq = 1
23 case 'p': m_msg->qdnaseq = 0;
24 case 'O': m_msg->outfile
26 case 'Q': m_msg->quiet = 1;
27 case 'r': ppst->p_d_mat,&ppst->p_d_mis
28 case 'R': m_msg->dfile
29 case 's': standard_pam(smstr); ppst->pamoff=atoi(bp+1);
30 case 'S': ppst->ext_sq_set = 1;
31 case 't': ppst->tr_type
32 case 'T': PCOMPLIB: worker_1,worker_n
34 case 'v': ppst->zs_win
35 case 'w': m_msg->aln.llen
36 case 'W': m_msg->aln.llcntx);
37 case 'X': m_msg->sq0off,&m_msg->sq1off
39 case 'z': ppst->zsflag
40 case 'Z': ppst->zdb_size
43 case '1': ppst->param_u.fa.iniflag=1;
44 case '3': m_msg->nframe = 3; /* TFASTA */
45 m_msg->nframe = 1; /* for TFASTXY */
46 m_msg->qframe = 1; /* for FASTA, FASTX */
47 case 'A': ppst->sw_flag= 1;
48 case 'c': ppst->param_u.fa.optcut
49 case 'h': ppst->gshift
51 case 'o': ppst->param_u.fa.optflag = 0;
52 case 'y': ppst->param_u.fa.optwid
55 case '3': m_msg->qframe = m_msg->nframe = 1;