/**
* @brief FIXME add doc
*
*/
void
PrintUserOpts(FILE *prFile, cmdline_opts_t *opts) {
/* keep in same order as in struct. FIXME could this be derived from argtable?
*/
fprintf(prFile, "seq-type = %s\n", SeqTypeToStr(opts->iSeqType));
fprintf(prFile, "seq-in-fmt = %s\n", SeqfileFormat2String(opts->iSeqInFormat));
fprintf(prFile, "option: seq-in = %s\n",
NULL != opts->pcSeqInfile? opts->pcSeqInfile: "(null)");
fprintf(prFile, "option: dealign = %d\n", opts->bDealignInputSeqs);
fprintf(prFile, "option: profile1 = %s\n",
NULL != opts->pcProfile1Infile? opts->pcProfile1Infile: "(null)");
fprintf(prFile, "option: profile2 = %s\n",
NULL != opts->pcProfile2Infile? opts->pcProfile2Infile: "(null)");
fprintf(prFile, "option: max-num-seq = %d\n", opts->iMaxNumSeq);
fprintf(prFile, "option: max-seq-len = %d\n", opts->iMaxSeqLen);
fprintf(prFile, "option: aln-out-file = %s\n",
NULL != opts->pcAlnOutfile? opts->pcAlnOutfile: "(null)");
fprintf(prFile, "option: aln-out-format = %s\n", SeqfileFormat2String(opts->iAlnOutFormat));
fprintf(prFile, "option: force-file-overwrite = %d\n", opts->bForceFileOverwrite);
fprintf(prFile, "option: threads = %d\n", opts->iThreads);
fprintf(prFile, "option: logFile = %s\n", opts->pcLogFile);
}
/* Function: MSAFileFormat()
* Date: SRE, Fri Jun 18 14:26:49 1999 [Sanger Centre]
*
* Purpose: (Attempt to) determine the format of an alignment file.
* Since it rewinds the file pointer when it's done,
* cannot be used on a pipe or gzip'ed file. Works by
* calling SeqfileFormat() from sqio.c, then making sure
* that the format is indeed an alignment. If the format
* comes back as FASTA, it assumes that the format as A2M
* (e.g. aligned FASTA).
*
* Args: fname - file to evaluate
*
* Returns: format code; e.g. MSAFILE_STOCKHOLM
*/
int
MSAFileFormat(MSAFILE *afp)
{
int fmt;
fmt = SeqfileFormat(afp->f);
if (fmt == SQFILE_FASTA) fmt = MSAFILE_A2M;
if (fmt != MSAFILE_UNKNOWN && ! IsAlignmentFormat(fmt))
Die("File %s does not appear to be an alignment file;\n\
rather, it appears to be an unaligned file in %s format.\n\
I'm expecting an alignment file in this context.\n",
afp->fname,
SeqfileFormat2String(fmt));
return fmt;
}
