/** * @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; }