C++ (Cpp) gt_option_new_long示例

示例#1

文件： gt_packedindex_chk_search.c 项目： simongog/genometools

static GtOPrval
parseChkBWTOptions(int *parsed_args, int argc, const char **argv,
                   struct chkSearchOptions *params, const GtStr *projectName,
                   GtError *err)
{
  GtOptionParser *op;
  GtOPrval oprval;
  GtOption *option, *optionProgress;
  bool checkSuffixArrayValues, tryContextRetrieve, tryFullRegen;

  gt_error_check(err);
  op = gt_option_parser_new("indexname",
                         "Load (or build if necessary) BWT index for project"
                         " <indexname> and perform verification of search"
                         " results.");

  gt_registerPackedIndexOptions(op, &params->idx, BWTDEFOPT_MULTI_QUERY,
                             projectName);

  option = gt_option_new_long("minpatlen",
                           "minimum length of patterns searched for, -1 "
                           "implies automatic choice based on index "
                           "properties", &params->minPatLen, -1);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_long("maxpatlen",
                           "maximum length of patterns searched for, -1 "
                           "implies automatic choice based on index "
                           "properties", &params->maxPatLen, -1);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong("nsamples",
                            "number of sequences to search for",
                            &params->numOfSamples, 1000);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("chksfxarray",
                           "verify integrity of stored suffix array positions",
                           &checkSuffixArrayValues, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("full-lfmap",
                           "verify complete backwards regeneration of "
                           "original sequence", &tryFullRegen, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("chkcontext",
                           "verify integrity of regenerated sequence context",
                           &tryContextRetrieve, false);
  gt_option_parser_add_option(op, option);

  optionProgress = gt_option_new_ulong("ticks",
                                    "print dot after this many symbols "
                                    "tested okay", &params->progressInterval,
                                    DEFAULT_PROGRESS_INTERVAL);
  gt_option_parser_add_option(op, optionProgress);

  option = gt_option_new_bool("v",
                           "print verbose progress information",
                           &params->verboseOutput,
                           false);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_max_args(op, 1, 1);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);

  /* condense boolean options to flags field */
  params->flags = (checkSuffixArrayValues?VERIFY_BWTSEQ_SUFVAL:0)
    | (tryFullRegen?VERIFY_BWTSEQ_LFMAPWALK:0)
    | (tryContextRetrieve?VERIFY_BWTSEQ_CONTEXT:0);
  /* compute parameters currently not set from command-line or
   * determined indirectly */
  gt_computePackedIndexDefaults(&params->idx, BWTBaseFeatures);

  gt_option_parser_delete(op);

  return oprval;
}

示例#2

static GtOptionParser *gt_idxlocali_option_parser_new (void *tool_arguments)
{
  IdxlocaliOptions *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *optionesaindex, *optionpckindex, *optiononline, *optioncmp;

  gt_assert (arguments != NULL);
  arguments->indexname = gt_str_new ();
  arguments->queryfiles = gt_str_array_new ();

  op = gt_option_parser_new
    ("[options] -q query-file-names [-esa|-pck] indexname",
     "Find all local alignments using suffix tree.");

  gt_option_parser_set_mailaddress (op, "<*****@*****.**>");
  option = gt_option_new_filenamearray ("q","Specify files containing the "
                                            "query sequences",
                                        arguments->queryfiles);
  gt_option_parser_add_option (op, option);

  option = gt_option_new_long ("match",
                               "Specify match score",
                               &arguments->matchscore, 1L);
  gt_option_parser_add_option (op, option);

  option = gt_option_new_long ("mismatch",
                               "Specify mismatch score",
                               &arguments->mismatchscore, -3L);
  gt_option_parser_add_option (op, option);

  option = gt_option_new_long ("gapstart",
                               "Specify gap start score",
                               &arguments->gapstart, -5L);
  gt_option_parser_add_option (op, option);

  option = gt_option_new_long ("gapextend",
                               "Specify gap extension score",
                               &arguments->gapextend, -2L);
  gt_option_parser_add_option (op, option);

  option = gt_option_new_ulong_min ("th",
                                    "Specify the threshold",
                                     &arguments->threshold, 0, 1UL);
  gt_option_parser_add_option (op, option);
  gt_option_is_mandatory (option);

  optionesaindex = gt_option_new_string ("esa",
                                         "Specify index "
                                         "(enhanced suffix array)",
                                         arguments->indexname, NULL);
  gt_option_parser_add_option (op, optionesaindex);
  arguments->refoptionesaindex = gt_option_ref (optionesaindex);

  optionpckindex = gt_option_new_string ("pck",
                                         "Specify index (packed index)",
                                         arguments->indexname, NULL);
  gt_option_parser_add_option (op, optionpckindex);
  arguments->refoptionpckindex = gt_option_ref (optionpckindex);
  gt_option_exclude (optionesaindex, optionpckindex);
  gt_option_is_mandatory_either (optionesaindex, optionpckindex);

  optiononline = gt_option_new_bool("online","Perform online searches",
                                    &arguments->doonline, false);
  gt_option_parser_add_option(op, optiononline);
  gt_option_is_development_option(optiononline);

  optioncmp = gt_option_new_bool("cmp","Compare results of offline and online "
                                 "searches",
                                 &arguments->docompare, false);
  gt_option_parser_add_option(op,optioncmp);
  gt_option_exclude(optiononline,optioncmp);

  option = gt_option_new_bool("s",
                              "Show alignments",
                              &arguments->showalignment, false);
  gt_option_parser_add_option (op, option);

  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);
  return op;
}