hmmer-3.3/src/fm_general.c
/*********************************************************************
 *# 4. FM data initialization, configuration, and reading from file
 *********************************************************************/
# 4. FM data initialization, configuration, and reading from file
# 4 . FM data initialization configuration and reading from file
int
fm_initConfigGeneric( FM_CFG *cfg, ESL_GETOPTS *go ) {
  cfg->ssv_length        = (go ? esl_opt_GetInteger(go, "--seed_ssv_length") : -1);
  cfg->max_depth         = (go ? esl_opt_GetInteger(go, "--seed_max_depth") :  -1);
  cfg->drop_max_len      = (go ? esl_opt_GetInteger(go, "--seed_drop_max_len") : -1);
  cfg->consec_pos_req    = (go ? esl_opt_GetInteger(go, "--seed_req_pos") : -1);
  cfg->consensus_match_req = (go ? esl_opt_GetInteger(go, "--seed_consens_match") : 10);
  cfg->drop_lim          = eslCONST_LOG2 * (go ? esl_opt_GetReal(go, "--seed_drop_lim") : -1.0);  
  cfg->score_density_req = eslCONST_LOG2 * (go ? esl_opt_GetReal(go, "--seed_sc_density") : -1.0);
  cfg->scthreshFM        = eslCONST_LOG2 * (go ? esl_opt_GetReal(go, "--seed_sc_thresh") : -1.0); 
  return eslOK;
}
int fm_initConfigGeneric ( FM_CFG * cfg , ESL_GETOPTS * go ) { cfg -> ssv_length = ( go ? esl_opt_GetInteger ( go , " " ) : -1 ) ; cfg -> max_depth = ( go ? esl_opt_GetInteger ( go , " " ) : -1 ) ; cfg -> drop_max_len = ( go ? esl_opt_GetInteger ( go , " " ) : -1 ) ; cfg -> consec_pos_req = ( go ? esl_opt_GetInteger ( go , " " ) : -1 ) ; cfg -> consensus_match_req = ( go ? esl_opt_GetInteger ( go , " " ) : 10 ) ; cfg -> drop_lim = eslCONST_LOG2 * ( go ? esl_opt_GetReal ( go , " " ) : -1.0 ) ; cfg -> score_density_req = eslCONST_LOG2 * ( go ? esl_opt_GetReal ( go , " " ) : -1.0 ) ; cfg -> scthreshFM = eslCONST_LOG2 * ( go ? esl_opt_GetReal ( go , " " ) : -1.0 ) ; return eslOK ; }
# 4.
# 4 .
// convert from bits to nats // convert from bits to nats // convert from bits to nats