C++ (Cpp) gth_get_time Exemples

Exemple #1

Fichier : run_header.c Projet : AlexWoroschilow/uni_hamburg

void gth_run_header_show(GthCallInfo *call_info, GthInput *input,
                         const char *gth_version, unsigned int indentlevel,
                         const char **args)
{
  char *timestring;
  GtFile *outfp = call_info->out->outfp;

  /* determine time */
  timestring = gth_get_time();

  /* output XML header */
  if (call_info->out->xmlout) {
    show_xml_run_header(call_info, input, timestring, gth_version, indentlevel,
                        args);
  }
  else if (!call_info->out->gff3out) {
    gt_file_xprintf(outfp, "%c GenomeThreader %s (%s)\n", COMMENTCHAR,
                    gth_version, GT_BUILT);
    gt_file_xprintf(outfp, "%c Date run: %s\n", COMMENTCHAR, timestring);
    gt_file_xprintf(outfp, "%c Arguments: ", COMMENTCHAR);
    gt_cstr_array_show_genfile(args, outfp);
  }

  /* free */
  gt_free(timestring);
}

Exemple #2

Fichier : stat.c Projet : 9beckert/TIR

void gth_stat_show(GthStat *stat, bool show_full_stats, bool xmlout,
                   GtFile *outfp)
{
  char *timestring;

  gt_assert(stat);

  /* begin XML comment */
  if (xmlout)
    gt_file_xprintf(outfp, "<!--\n");

  /* output exon length distribution */
  if (stat->exondistri) {
    gt_file_xprintf(outfp, "%c length distribution of all exons:\n",
                    COMMENTCHAR);
    gt_disc_distri_show(stat->exondistribution, outfp);
  }

  /* output intron length distribution */
  if (stat->introndistri) {
    if (stat->exondistri)
      gt_file_xprintf(outfp, "%c\n", COMMENTCHAR);
    gt_file_xprintf(outfp, "%c length distribution of all introns:\n",
                    COMMENTCHAR);
    gt_disc_distri_show(stat->introndistribution, outfp);
  }

  /* output match number distribution */
  if (stat->matchnumdistri) {
    if (stat->exondistri || stat->introndistri)
      gt_file_xprintf(outfp, "%c\n", COMMENTCHAR);
    gt_file_xprintf(outfp, "%c distribution of match numbers (per genomic "
                    "file, per reference sequence:\n", COMMENTCHAR);
    gt_disc_distri_show(stat->matchnumdistribution, outfp);
  }

  /* output reference sequence coverage distribution */
  if (stat->refseqcovdistri) {
    if (stat->exondistri || stat->introndistri || stat->matchnumdistri)
      gt_file_xprintf(outfp, "%c\n", COMMENTCHAR);
    gt_file_xprintf(outfp, "%c reference sequence coverage distribution (of "
                    "global chains):\n", COMMENTCHAR);
    gt_disc_distri_show(stat->refseqcoveragedistribution, outfp);
  }

  /* output spliced alignment statistics */
  if (stat->sa_stats) {
    if (stat->exondistri     || stat->introndistri ||
        stat->matchnumdistri || stat->refseqcovdistri) {
      gt_file_xprintf(outfp, "%c\n", COMMENTCHAR);
    }
    INFOCHAR;
    gt_file_xprintf(outfp,
                       "spliced alignment alignment score distribution:\n");
    gt_disc_distri_show(stat->sa_alignment_score_distribution, outfp);
    INFOCHAR;
    gt_file_xfputc('\n', outfp);
    INFOCHAR;
    gt_file_xprintf(outfp, "spliced alignment coverage distribution:\n");
    gt_disc_distri_show(stat->sa_coverage_distribution, outfp);
  }

  /* output general statistics */
  outputgeneralstatistics(stat, show_full_stats, outfp);
  INFOCHAR;
  gt_file_xfputc('\n', outfp);

  /* output the memory statistics */
  outputmemorystatistics(stat, show_full_stats, outfp);

  /* output time */
  INFOCHAR;
  gt_file_xfputc('\n', outfp);
  INFOCHAR;
  timestring = gth_get_time();
  gt_file_xprintf(outfp, "date finished: %s\n", timestring);
  gt_free(timestring);

  /* output important messages */
  if (stat->numofremovedzerobaseexons         ||
      stat->numofautointroncutoutcalls        ||
      stat->numofunsuccessfulintroncutoutDPs  ||
      stat->numoffailedDPparameterallocations ||
      stat->numoffailedmatrixallocations      ||
      stat->numofundeterminedSAs              ||
      stat->numoffilteredpolyAtailmatches) {
    gt_file_xprintf(outfp, "%c\n", COMMENTCHAR);
    gt_file_xprintf(outfp, "%c important messages:\n", COMMENTCHAR);
    if (stat->numofremovedzerobaseexons > 0) {
      gt_file_xprintf(outfp, "%c %lu removed zero base exons\n",
                         COMMENTCHAR, stat->numofremovedzerobaseexons);
    }
    if (stat->numofautointroncutoutcalls > 0) {
      gt_file_xprintf(outfp, "%c %lu times the intron cutout technique was "
                         "used automatically\n", COMMENTCHAR,
                         stat->numofautointroncutoutcalls);
    }
    if (stat->numofunsuccessfulintroncutoutDPs > 0) {
      gt_file_xprintf(outfp, "%c %lu unsuccessful DP calls using intron "
                         "cutout technique\n", COMMENTCHAR,
                         stat->numofunsuccessfulintroncutoutDPs);
    }
    if (stat->numoffailedDPparameterallocations > 0) {
      gt_file_xprintf(outfp, "%c %lu DP parameter allocations failed\n",
                         COMMENTCHAR, stat->numoffailedDPparameterallocations);
    }
    if (stat->numoffailedmatrixallocations > 0) {
      gt_file_xprintf(outfp, "%c %lu matrix allocations failed\n",
                         COMMENTCHAR, stat->numoffailedmatrixallocations);
    }
    if (stat->numofundeterminedSAs > 0) {
      gt_file_xprintf(outfp, "%c %lu undetermined spliced alignments\n",
                         COMMENTCHAR, stat->numofundeterminedSAs);
    }
    if (stat->numoffilteredpolyAtailmatches > 0) {
      gt_file_xprintf(outfp,
                      "%c %lu matches containing a poly(A) tail filtered\n",
                         COMMENTCHAR, stat->numoffilteredpolyAtailmatches);
    }
  }

  /* end XML comment */
  if (xmlout)
    gt_file_xprintf(outfp, "-->\n");
}