static void bgp_setup_conn(struct bgp_proto *p, struct bgp_conn *conn) { timer *t; conn->sk = NULL; conn->bgp = p; conn->packets_to_send = 0; t = conn->connect_retry_timer = tm_new(p->p.pool); t->hook = bgp_connect_timeout; t->data = conn; t = conn->hold_timer = tm_new(p->p.pool); t->hook = bgp_hold_timeout; t->data = conn; t = conn->keepalive_timer = tm_new(p->p.pool); t->hook = bgp_keepalive_timeout; t->data = conn; conn->tx_ev = ev_new(p->p.pool); conn->tx_ev->hook = bgp_kick_tx; conn->tx_ev->data = conn; }
int main(int argc, char *argv[]) { struct TM *tm; char *symbols; int n_states, n_syms; int *new_states; char *new_syms, *new_dirs; int n_tuples; char dir; FILE *program; char *tape_buffer; size_t tape_size = 1024; ssize_t tape_read; if (argc < 2) { fprintf(stderr, "usage: %s [program.tur]\n", argv[0]); return 1; } else if ((program = fopen(argv[1], "r")) == NULL) { const char *errstr = strerror(errno); fprintf(stderr, "%s: %s\n", argv[1], errstr); return 1; } fscanf(program, "%d %d", &n_states, &n_syms); n_tuples = n_states * n_syms; symbols = malloc(n_syms+1); symbols[n_syms] = 0; fscanf(program, "%s", symbols); if (debug) printf("states: %d, symbols(%d): %s\n", n_states, n_syms, symbols); new_states = malloc(sizeof(*new_states) * n_tuples); new_syms = malloc(n_tuples); new_dirs = malloc(n_tuples); for (int i=0; i<n_tuples; ++i) { fscanf(program, "%d %c %c", new_states+i, new_syms+i, &dir); new_dirs[i] = dir == '+' ? 1 : -1; if (debug) printf("(%d %c) -> (%d %c %c)\n", i/n_syms, symbols[i%n_syms], new_states[i], new_syms[i], dir); } tm = tm_new(symbols, new_states, new_syms, new_dirs, n_states, n_syms); // read tape from standard in tape_buffer = malloc(tape_size); tape_read = getline(&tape_buffer, &tape_size, stdin); if (tape_read < 1 || tape_buffer[0] == '\n') fprintf(stderr, "no tape given\n"); else { tape_buffer[tape_read-1] = 0; tm_init(tm, 0, 0, tape_buffer); tm_run(tm); } fclose(program); free(new_states); free(new_syms); free(new_dirs); return 0; }
int main(int argc, char *argv[]) { TreeNode *tree = NULL; TreeModel *backgd_mod = NULL; int i, j, size = DEFAULT_SIZE, meme_mode = 0, profile_mode = 0, nrestarts = 10, npseudocounts = 5, nsamples = -1, nmostprevalent = -1, tuple_size = -1, nbest = -1, sample_parms = 0, nmotifs = DEFAULT_NUMBER, nseqs = -1, do_html = 0, do_bed = 0, suppress_stdout = 0; List *msa_name_list = NULL, *pos_examples = NULL, *init_list = NULL, *tmpl; List *msas, *motifs; SeqSet *seqset = NULL; PooledMSA *pmsa = NULL; msa_format_type msa_format = UNKNOWN_FORMAT; Vector *backgd_mnmod = NULL; Hashtable *hash=NULL; String *output_prefix = str_new_charstr("phastm."); double *has_motif = NULL; double prior = PRIOR; char c; GFF_Set *bedfeats = NULL; while ((c = getopt(argc, argv, "t:i:b:sk:md:pn:I:R:P:w:c:SB:o:HDxh")) != -1) { switch (c) { case 't': tree = tr_new_from_file(phast_fopen(optarg, "r")); break; case 'i': msa_format = msa_str_to_format(optarg); if (msa_format == UNKNOWN_FORMAT) die("ERROR: bad input format.\n"); break; case 'b': backgd_mod = tm_new_from_file(phast_fopen(optarg, "r"), 1); break; case 's': break; case 'k': size = get_arg_int(optarg); break; case 'm': meme_mode = 1; break; case 'd': pos_examples = get_arg_list(optarg); break; case 'p': profile_mode = 1; break; case 'n': nrestarts = get_arg_int(optarg); break; case 'I': init_list = get_arg_list(optarg); break; case 'P': tmpl = str_list_as_int(get_arg_list(optarg)); if (lst_size(tmpl) != 2) die("ERROR: bad argument to -P.\n"); nmostprevalent = lst_get_int(tmpl, 0); tuple_size = lst_get_int(tmpl, 1); if (!(nmostprevalent > 0 && tuple_size > 0)) die("ERROR: bad argument nmostprevalent=%i tuple_size=%i\n", nmostprevalent, tuple_size); lst_free(tmpl); break; case 'R': tmpl = str_list_as_int(get_arg_list(optarg)); if (lst_size(tmpl) != 2) die("ERROR: bad argument to -R.\n"); nsamples = lst_get_int(tmpl, 0); tuple_size = lst_get_int(tmpl, 1); if (!(nsamples > 0 && tuple_size > 0)) die("ERROR nsamples=%i tuple_sizse=%i\n", nsamples, tuple_size); lst_free(tmpl); break; case 'c': npseudocounts = get_arg_int(optarg); break; case 'w': nbest = get_arg_int(optarg); break; case 'S': sample_parms = 1; break; case 'B': nmotifs = get_arg_int(optarg); break; case 'o': str_free(output_prefix); output_prefix = str_new_charstr(optarg); str_append_char(output_prefix, '.'); break; case 'H': do_html = 1; break; case 'D': do_bed = 1; break; case 'x': suppress_stdout = 1; break; case 'h': usage(argv[0]); case '?': die("Bad argument. Try '%s -h'.\n", argv[0]); } } if (optind != argc - 1) die("ERROR: List of alignment files required. Try '%s -h'.\n", argv[0]); if ((nsamples > 0 && nmostprevalent > 0) || (nsamples > 0 && init_list != NULL) || (nmostprevalent > 0 && init_list != NULL)) die("ERROR: -I, -P, and -R are mutually exclusive."); set_seed(-1); msa_name_list = get_arg_list(argv[optind]); if (backgd_mod != NULL && tree == NULL) tree = backgd_mod->tree; if (tree == NULL && !meme_mode && !profile_mode) die("ERROR: Must specify -t, -m, or -p.\n"); if ((init_list != NULL || nsamples > 0 || nmostprevalent > 0) && !sample_parms) nrestarts = 1; if (pos_examples != NULL) { hash = hsh_new(lst_size(pos_examples)); for (i = 0; i < lst_size(pos_examples); i++) hsh_put_int(hash, ((String*)lst_get_ptr(pos_examples, i))->chars, 1); has_motif = smalloc(lst_size(msa_name_list) * sizeof(double)); } /* open all MSAs */ msas = lst_new_ptr(lst_size(msa_name_list)); fprintf(stderr, "Reading alignment(s) ...\n"); for (i = 0, j = 0; i < lst_size(msa_name_list); i++) { String *name = lst_get_ptr(msa_name_list, i); FILE *mfile = phast_fopen(name->chars, "r"); msa_format_type temp_format; MSA *msa; if (msa_format == UNKNOWN_FORMAT) temp_format = msa_format_for_content(mfile, 1); else temp_format = msa_format; msa = msa_new_from_file_define_format(mfile, temp_format, NULL); phast_fclose(mfile); if (nseqs == -1) nseqs = msa->nseqs; if (!meme_mode && (msa->length - msa_num_gapped_cols(msa, STRIP_ANY_GAPS, -1, -1) < 300 || msa->nseqs != nseqs)) { fprintf(stderr, "WARNING: ignoring alignment '%s' -- too few informative sites.\n", name->chars); msa_free(msa); continue; } if (msa_alph_has_lowercase(msa)) msa_toupper(msa); msa_remove_N_from_alph(msa); /* Ns can be a problem */ lst_push_ptr(msas, msa); if (has_motif != NULL) { int k, hm = (hsh_get_int(hash, name->chars) == 1); if (meme_mode) { /* here need to record at individ seq level */ has_motif = srealloc(has_motif, (j + msa->nseqs + 1) * sizeof(double)); /* FIXME */ for (k = 0; k < msa->nseqs; k++) has_motif[j++] = hm; } else has_motif[j++] = hm; } } if (!meme_mode) { fprintf(stderr, "Extracting and pooling sufficient statistics ...\n"); pmsa = ss_pooled_from_msas(msas, 1, size, NULL, 0); msa_remove_N_from_alph(pmsa->pooled_msa); } /* obtain individual sequences, if necessary */ if (nmostprevalent > 0 || nsamples > 0 || meme_mode) { if (meme_mode) fprintf(stderr, "Converting to individual sequences ...\n"); else fprintf(stderr, "Obtaining reference sequences for pre-processing ...\n"); seqset = mtf_get_seqset(msas, meme_mode ? -1 : 1, 10 * size); /* for now, assume 1st seq is reference */ msa_remove_N_from_alph(seqset->set); } if (nmostprevalent > 0) { fprintf(stderr, "Obtaining %d most prevalent %d-tuples ...\n", nmostprevalent, tuple_size); init_list = lst_new_ptr(nmostprevalent); mtf_get_common_ntuples(seqset, init_list, tuple_size, nmostprevalent); } else if (nsamples > 0) { fprintf(stderr, "Sampling %d %d-tuples ...\n", nsamples, tuple_size); init_list = lst_new_ptr(nsamples); mtf_sample_ntuples(seqset, init_list, tuple_size, nsamples); } /* in meme_mode, backgd model can be specified as eq freqs in a .mod file */ if (meme_mode && backgd_mod != NULL && has_motif == NULL) backgd_mnmod = backgd_mod->backgd_freqs; /* estimate background model, if necessary */ else if (backgd_mod == NULL && (!meme_mode || has_motif == NULL)) { fprintf(stderr, "Fitting background model%s ...\n", has_motif == NULL ? "" : " (for use in initialization)"); /* if discriminative, be clear backgd isn't really part of the estimation procedure */ if (meme_mode) { backgd_mnmod = vec_new(strlen(seqset->set->alphabet)); mtf_estim_backgd_mn(seqset, backgd_mnmod); } else { backgd_mod = tm_new(tr_create_copy(tree), NULL, NULL, F81, pmsa->pooled_msa->alphabet, 1, 0, NULL, -1); tm_fit(backgd_mod, pmsa->pooled_msa, tm_params_init(backgd_mod, .1, 5, 0), -1, OPT_MED_PREC, NULL, 0, NULL); } } /* select subset of init strings, if necessary */ if (nbest > 0 && init_list != NULL) { fprintf(stderr, "Winnowing candidate start strings ...\n"); tmpl = lst_new_ptr(nbest); mtf_winnow_starts(meme_mode ? (void*)seqset : (void*)pmsa, init_list, nbest, tmpl, !meme_mode, size, tree, meme_mode ? (void*)backgd_mnmod : (void*)backgd_mod, has_motif); lst_free(init_list); init_list = tmpl; } /* Now find motifs */ motifs = mtf_find(meme_mode ? (void*)seqset : (void*)pmsa, !meme_mode, size, nmotifs, tree, meme_mode ? (void*)backgd_mnmod : (void*)backgd_mod, has_motif, prior, nrestarts, init_list, sample_parms, npseudocounts); fprintf(stderr, "\n\n"); if (do_bed) bedfeats = gff_new_set_init("phast_motif", "0.1b"); /* generate output */ for (i = 0; i < lst_size(motifs); i++) { Motif *m = lst_get_ptr(motifs, i); if (!suppress_stdout) { if (lst_size(motifs) > 1) printf("\n**********\nMOTIF #%d\n**********\n\n", i+1); mtf_print(stdout, m); } if (do_html) { String *fname = str_dup(output_prefix); str_append_int(fname, i+1); str_append_charstr(fname, ".html"); mtf_print_html(phast_fopen(fname->chars, "w+"), m); str_free(fname); } if (do_bed) mtf_add_features(m, bedfeats); } if (do_html) { String *fname = str_dup(output_prefix); str_append_charstr(fname, "index.html"); mtf_print_summary_html(phast_fopen(fname->chars, "w+"), motifs, output_prefix); str_free(fname); } if (do_bed) { String *fname = str_dup(output_prefix); str_append_charstr(fname, "bed"); gff_print_bed(phast_fopen(fname->chars, "w+"), bedfeats, FALSE); str_free(fname); } return 0; }