+++ /dev/null
-doinit.c
- case 'a': m_msg->aln.showall = 1;
- case 'B': m_msg->z_bits = 0;
- case 'b': m_msg->mshow
- case 'C': m_msg->nmlen
- case 'd': m_msg->ashow);
- case 'D': ppst->debug_lib = 1;
- case 'E': m_msg->e_cut
- case 'F': m_msg->e_low
- case 'f': ppst->gdelval
- case 'g': ppst->ggapval
- case 'H': m_msg->nohist = 1; break;
- case 'i': m_msg->revcomp = 1; break;
- case 'I': m_msg->self = 1; break;
- case 'J': m_msg->ql_start, ql_stop
- case 'K': max_buf_cnt (PCOMPLIB)
- case 'l': m_msg->flstr
- case 'L': m_msg->long_info = 1
- case 'M': m_msg->n1_low,&m_msg->n1_high
- case 'm': m_msg->markx
- case 'n': m_msg->qdnaseq = 1
- case 'N': m_msg->maxn
- case 'p': m_msg->qdnaseq = 0;
- case 'O': m_msg->outfile
- case 'q':
- case 'Q': m_msg->quiet = 1;
- case 'r': ppst->p_d_mat,&ppst->p_d_mis
- case 'R': m_msg->dfile
- case 's': standard_pam(smstr); ppst->pamoff=atoi(bp+1);
- case 'S': ppst->ext_sq_set = 1;
- case 't': ppst->tr_type
- case 'T': PCOMPLIB: worker_1,worker_n
- _t: max_workers
- case 'v': ppst->zs_win
- case 'w': m_msg->aln.llen
- case 'W': m_msg->aln.llcntx);
- case 'X': m_msg->sq0off,&m_msg->sq1off
- case 'x': ppst->pam_x
- case 'z': ppst->zsflag
- case 'Z': ppst->zdb_size
-
-initfa.c
- case '1': ppst->param_u.fa.iniflag=1;
- case '3': m_msg->nframe = 3; /* TFASTA */
- m_msg->nframe = 1; /* for TFASTXY */
- m_msg->qframe = 1; /* for FASTA, FASTX */
- case 'A': ppst->sw_flag= 1;
- case 'c': ppst->param_u.fa.optcut
- case 'h': ppst->gshift
- case 'j': ppst->gsubs
- case 'o': ppst->param_u.fa.optflag = 0;
- case 'y': ppst->param_u.fa.optwid
-
-initsw.c
- case '3': m_msg->qframe = m_msg->nframe = 1;