int
process_searchopts(int fd, char *cmdstr, ESL_GETOPTS **ret_opts)
{
int status;
ESL_GETOPTS *go = NULL;
if ((go = esl_getopts_Create(searchOpts)) == NULL) return eslEMEM;
if ((status = esl_opt_ProcessSpoof(go, cmdstr)) != eslOK) return status;
if ((status = esl_opt_VerifyConfig(go)) != eslOK) return status;
*ret_opts = go;
return eslOK;
}
P7_HMM * constructHMM(ESL_MSA *msa, ESL_ALPHABET *abc, int ali_hmm, int frag, P7_HMM **ret_hmm, char *errbuf){
int status;
ESL_GETOPTS *go = esl_getopts_Create(options);
P7_BUILDER *bld = NULL;
P7_BG *bg = NULL;
char *args = NULL;
esl_strcat(&args, -1, "X ", -1);
status = esl_msa_SetName(msa, "Query", -1);
/* Now take this alignment and make an HMM from it */
if(status != eslOK){
ESL_XFAIL(status, errbuf, "Easel MSA SetNAME returned an error %d\n", status);
}
bg = p7_bg_Create(abc);
if(bg == NULL){
ESL_XFAIL(status, errbuf, "Error generating bg\n");
}
if (frag == 1) {
// add --fragthresh 0
esl_strcat(&args, -1, "--fragthresh 0 ", -1);
}
// if these flags are set, then we want a non standard hmm out. Used by the logo server.
if (ali_hmm == 1) {
// observed counts
// arguments "X --pnone --wnone --enone"
esl_strcat(&args, -1, "--pnone --wnone --enone --symfrac 0 ", -1);
}
else if (ali_hmm == 2) {
// weighted counts
// arguments "X --pnone");
esl_strcat(&args, -1, "--pnone --symfrac 0 ", -1);
}
else if (ali_hmm == 3) {
// Create HMM - keep all columns
esl_strcat(&args, -1, "--symfrac 0 ", -1);
}
else {
// no arguments ?
}
// pass in arguments to hmm builder
esl_opt_ProcessSpoof(go, args);
if (args != NULL) free(args);
bld = p7_builder_Create(go, abc);
if(bld == NULL){
ESL_XFAIL(eslEMEM, errbuf, "Error creating builder\n");
}
status = p7_Builder(bld, msa, bg, ret_hmm, NULL, NULL, NULL, NULL);
if (status != eslOK) {
strcpy( errbuf, bld->errbuf );
goto ERROR;
}
p7_bg_Destroy(bg);
p7_builder_Destroy(bld);
esl_getopts_Destroy(go);
return status;
ERROR:
if (bg != NULL) p7_bg_Destroy(bg);
if (bld != NULL) p7_builder_Destroy(bld);
if (go != NULL) esl_getopts_Destroy(go);
return status;
}