clustal-omega-1.2.4/src/mymain.c
/**
 * @brief Sets default user/commandline options
 *
 * @param[out] opts
 * The option structure to initialise
 *
 */
@brief Sets default user/commandline options

@param[out] opts
The option structure to initialise
@brief Sets default user / commandline options @param [ out ] opts The option structure to initialise
void
SetDefaultUserOpts(cmdline_opts_t *opts)
{
    assert(NULL != opts);
    opts->iSeqType = SEQTYPE_UNKNOWN;
    opts->pcSeqInfile = NULL;
    opts->bDealignInputSeqs = FALSE;        
    opts->pcProfile1Infile = NULL;
    opts->pcProfile2Infile = NULL;
    opts->bIsProfile = FALSE;
    opts->aln_opts.bUseKimura = FALSE;
	opts->aln_opts.bPercID = FALSE;
    opts->aln_opts.pcHMMBatch = NULL;
    opts->iMaxNumSeq = INT_MAX;
    opts->iMaxSeqLen = INT_MAX;
    opts->pcAlnOutfile = NULL;
    opts->iAlnOutFormat =  MSAFILE_A2M;
    opts->bForceFileOverwrite = FALSE;
    opts->iWrap = 60;
    opts->bResno = FALSE;
    opts->iOutputOrder = INPUT_ORDER;
#ifdef HAVE_OPENMP
    opts->iThreads = omp_get_max_threads();
#else
    opts->iThreads = 1;
#endif
    opts->pcPseudoFile = NULL;
    opts->pcLogFile = NULL;
    SetDefaultAlnOpts(& opts->aln_opts);
}
void SetDefaultUserOpts ( cmdline_opts_t * opts ) { assert ( NULL != opts ) ; opts -> iSeqType = SEQTYPE_UNKNOWN ; opts -> pcSeqInfile = NULL ; opts -> bDealignInputSeqs = FALSE ; opts -> pcProfile1Infile = NULL ; opts -> pcProfile2Infile = NULL ; opts -> bIsProfile = FALSE ; opts -> aln_opts . bUseKimura = FALSE ; opts -> aln_opts . bPercID = FALSE ; opts -> aln_opts . pcHMMBatch = NULL ; opts -> iMaxNumSeq = INT_MAX ; opts -> iMaxSeqLen = INT_MAX ; opts -> pcAlnOutfile = NULL ; opts -> iAlnOutFormat = MSAFILE_A2M ; opts -> bForceFileOverwrite = FALSE ; opts -> iWrap = 60 ; opts -> bResno = FALSE ; opts -> iOutputOrder = INPUT_ORDER ; #ifdef HAVE_OPENMP opts -> iThreads = omp_get_max_threads ( ) ; #else opts -> iThreads = 1 ; #endif opts -> pcPseudoFile = NULL ; opts -> pcLogFile = NULL ; SetDefaultAlnOpts ( & opts -> aln_opts ) ; }
@brief Sets default user/commandline options
@brief Sets default user / commandline options
/* defaults to # of CPUs */