/* Function: p7_banner()
* Synopsis: print standard HMMER application output header
* Incept: SRE, Wed May 23 10:45:53 2007 [Janelia]
*
* Purpose: Print the standard HMMER command line application banner
* to <fp>, constructing it from <progname> (the name of the
* program) and a short one-line description <banner>.
* For example,
* <p7_banner(stdout, "hmmsim", "collect profile HMM score distributions");>
* might result in:
*
* \begin{cchunk}
* # hmmsim :: collect profile HMM score distributions
* # HMMER 3.0 (May 2007)
* # Copyright (C) 2004-2007 HHMI Janelia Farm Research Campus
* # Freely licensed under the Janelia Software License.
* # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
* \end{cchunk}
*
* <progname> would typically be an application's
* <argv[0]>, rather than a fixed string. This allows the
* program to be renamed, or called under different names
* via symlinks. Any path in the <progname> is discarded;
* for instance, if <progname> is "/usr/local/bin/hmmsim",
* "hmmsim" is used as the program name.
*
* Note:
* Needs to pick up preprocessor #define's from p7_config.h,
* as set by ./configure:
*
* symbol example
* ------ ----------------
* HMMER_VERSION "3.0"
* HMMER_DATE "May 2007"
* HMMER_COPYRIGHT "Copyright (C) 2004-2007 HHMI Janelia Farm Research Campus"
* HMMER_LICENSE "Freely licensed under the Janelia Software License."
*
* Returns: (void)
*/
void
p7_banner(FILE *fp, char *progname, char *banner)
{
char *appname = NULL;
if (esl_FileTail(progname, FALSE, &appname) != eslOK) appname = progname;
fprintf(fp, "# %s :: %s\n", appname, banner);
fprintf(fp, "# HMMER %s (%s); %s\n", HMMER_VERSION, HMMER_DATE, HMMER_URL);
fprintf(fp, "# %s\n", HMMER_COPYRIGHT);
fprintf(fp, "# %s\n", HMMER_LICENSE);
fprintf(fp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n");
if (appname != NULL) free(appname);
return;
}
static int
output_header(FM_METADATA *meta, FILE *ofp, const ESL_GETOPTS *go, char *fmfile, char *qfile)
{
char *alph;
char *appname = NULL;
int status;
if (meta->alph_type == fm_DNA) alph = "dna";
else if (meta->alph_type == fm_AMINO) alph = "amino";
if ((status = esl_FileTail(go->argv[0], FALSE, &appname)) != eslOK) return status;
if (fprintf(ofp, "# %s :: %s\n", appname, banner) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# %s\n", EASEL_COPYRIGHT) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# %s\n", EASEL_LICENSE) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# input binary-formatted HMMER database: %s\n", fmfile) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# input file of query sequences: %s\n", qfile) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--out")) {
char *outfile = esl_opt_GetString(go, "--out");
if (fprintf(ofp, "# output file containing list of hits: %s\n", (esl_strcmp(outfile, "-") == 0 ? "stdout" : outfile)) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
}
if (esl_opt_IsUsed(go, "--count_only") && fprintf(ofp, "# output only counts, not hit locations\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# alphabet : %s\n", alph) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# bin_length : %d\n", meta->freq_cnt_b) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# suffix array sample rate: %d\n", meta->freq_SA) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (appname) free(appname);
return eslOK;
ERROR:
if (appname) free(appname);
return status;
}
/* set_msa_name()
* Make sure the alignment has a name; this name will
* then be transferred to the model.
*
* We can only do this for a single alignment in a file. For multi-MSA
* files, each MSA is required to have a name already.
*
* Priority is:
* 1. Use -n <name> if set, overriding any name the alignment might already have.
* 2. Use alignment's existing name, if non-NULL.
* 3. Make a name, from alignment file name without path and without filename extension
* (e.g. "/usr/foo/globins.slx" gets named "globins")
* If none of these succeeds, return <eslEINVAL>.
*
* If a multiple MSA database (e.g. Stockholm/Pfam), and we encounter
* an MSA that doesn't already have a name, return <eslEINVAL> if nali > 1.
* (We don't know we're in a multiple MSA database until we're on the second
* alignment.)
*
* If we're in MPI mode, we assume we're in a multiple MSA database,
* even on the first alignment.
*
* Because we can't tell whether we've got more than one
* alignment 'til we're on the second one, these fatal errors
* only happen after the first HMM has already been built.
* Oh well.
*/
static int
set_msa_name(struct cfg_s *cfg, char *errbuf, ESL_MSA *msa)
{
char *name = NULL;
int status;
if (cfg->do_mpi == FALSE && cfg->nali == 1) /* first (only?) HMM in file: */
{
if (cfg->hmmName != NULL)
{
if ((status = esl_msa_SetName(msa, cfg->hmmName)) != eslOK) return status;
}
else if (msa->name != NULL)
{
cfg->nnamed++;
}
else if (! cfg->afp->do_stdin)
{
if ((status = esl_FileTail(cfg->afp->fname, TRUE, &name)) != eslOK) return status; /* TRUE=nosuffix */
if ((status = esl_msa_SetName(msa, name)) != eslOK) return status;
free(name);
}
else ESL_FAIL(eslEINVAL, errbuf, "Failed to set model name: msa has no name, no msa filename, and no -n");
}
else
{
if (cfg->hmmName != NULL) ESL_FAIL(eslEINVAL, errbuf, "Oops. Wait. You can't use -n with an alignment database.");
else if (msa->name != NULL) cfg->nnamed++;
else ESL_FAIL(eslEINVAL, errbuf, "Oops. Wait. I need name annotation on each alignment in a multi MSA file; failed on #%d", cfg->nali+1);
/* special kind of failure: the *first* alignment didn't have a name, and we used the filename to
* construct one; now that we see a second alignment, we realize this was a boo-boo*/
if (cfg->nnamed != cfg->nali) ESL_FAIL(eslEINVAL, errbuf, "Oops. Wait. I need name annotation on each alignment in a multi MSA file; first MSA didn't have one");
}
return eslOK;
}
