C++ (Cpp) gt_feature_node_score_is_defined示例

示例#1

文件： gff3_output.c 项目： AnnSeidel/genometools

void gt_gff3_output_leading_str(GtFeatureNode *fn, GtStr *outstr)
{
  GtGenomeNode *gn;
  gt_assert(fn && outstr);
  gn = (GtGenomeNode*) fn;
  gt_str_append_str(outstr, gt_genome_node_get_seqid(gn));
  gt_str_append_char(outstr, '\t');
  gt_str_append_cstr(outstr, gt_feature_node_get_source(fn));
  gt_str_append_char(outstr, '\t');
  gt_str_append_cstr(outstr, gt_feature_node_get_type(fn));
  gt_str_append_char(outstr, '\t');
  gt_str_append_uword(outstr, gt_genome_node_get_start(gn));
  gt_str_append_char(outstr, '\t');
  gt_str_append_uword(outstr, gt_genome_node_get_end(gn));
  gt_str_append_char(outstr, '\t');
  if (gt_feature_node_score_is_defined(fn)) {
    char buf[BUFSIZ];
    (void) snprintf(buf, BUFSIZ, "%.3g", gt_feature_node_get_score(fn));
    gt_str_append_cstr(outstr, buf);
  } else
    gt_str_append_char(outstr, '.');
  gt_str_append_char(outstr, '\t');
  gt_str_append_char(outstr, GT_STRAND_CHARS[gt_feature_node_get_strand(fn)]);
  gt_str_append_char(outstr, '\t');
  gt_str_append_char(outstr, GT_PHASE_CHARS[gt_feature_node_get_phase(fn)]);
  gt_str_append_char(outstr, '\t');
}

示例#2

文件： genome_node_lua.c 项目： kowsky/genometools

static int feature_node_lua_get_score(lua_State *L)
{
  GtGenomeNode **gn = check_genome_node(L, 1);
  GtFeatureNode *fn;
  /* make sure we get a feature node */
  fn = gt_feature_node_try_cast(*gn);
  luaL_argcheck(L, fn, 1, "not a feature node");
  if (gt_feature_node_score_is_defined(fn))
    lua_pushnumber(L, gt_feature_node_get_score(fn));
  else
    lua_pushnil(L);
  return 1;
}

示例#3

文件： stat_visitor.c 项目： ggonnella/genometools

static void compute_type_statistics(GtFeatureNode *fn, GtStatVisitor *sv)
{
  GtRange range;
  gt_assert(fn && sv);
  if (gt_feature_node_has_type(fn, gt_ft_gene)) {
    sv->number_of_genes++;
    if (gt_feature_node_has_CDS(fn))
      sv->number_of_protein_coding_genes++;
    if (sv->gene_length_distribution) {
      range = gt_genome_node_get_range((GtGenomeNode*) fn);
      gt_disc_distri_add(sv->gene_length_distribution, gt_range_length(&range));
    }
    if (sv->gene_score_distribution && gt_feature_node_score_is_defined(fn)) {
      gt_disc_distri_add(sv->gene_score_distribution,
                         gt_feature_node_get_score(fn) * 100.0);
    }
  }
  else if (gt_feature_node_has_type(fn, gt_ft_mRNA)) {
    sv->number_of_mRNAs++;
    if (gt_feature_node_has_CDS(fn))
      sv->number_of_protein_coding_mRNAs++;
  }
  else if (gt_feature_node_has_type(fn, gt_ft_exon)) {
    sv->number_of_exons++;
    if (sv->exon_length_distribution) {
      range = gt_genome_node_get_range((GtGenomeNode*) fn);
      gt_disc_distri_add(sv->exon_length_distribution,
                         gt_range_length(&range));
    }
  }
  else if (gt_feature_node_has_type(fn, gt_ft_CDS)) {
    sv->number_of_CDSs++;
  }
  else if (gt_feature_node_has_type(fn, gt_ft_intron)) {
    if (sv->intron_length_distribution) {
      range = gt_genome_node_get_range((GtGenomeNode*) fn);
      gt_disc_distri_add(sv->intron_length_distribution,
                         gt_range_length(&range));
    }
  }
  else if (gt_feature_node_has_type(fn, gt_ft_LTR_retrotransposon)) {
    sv->number_of_LTR_retrotransposons++;
  }
}

示例#4

文件： gff3_output.c 项目： AnnSeidel/genometools

void gt_gff3_output_leading(GtFeatureNode *fn, GtFile *outfp)
{
  GtGenomeNode *gn;
  gt_assert(fn);
  gn = (GtGenomeNode*) fn;
  gt_file_xprintf(outfp, "%s\t%s\t%s\t"GT_WU"\t"GT_WU"\t",
                     gt_str_get(gt_genome_node_get_seqid(gn)),
                     gt_feature_node_get_source(fn),
                     gt_feature_node_get_type(fn),
                     gt_genome_node_get_start(gn),
                     gt_genome_node_get_end(gn));
  if (gt_feature_node_score_is_defined(fn))
    gt_file_xprintf(outfp, "%.3g", gt_feature_node_get_score(fn));
  else
    gt_file_xfputc('.', outfp);
  gt_file_xprintf(outfp, "\t%c\t%c\t",
                     GT_STRAND_CHARS[gt_feature_node_get_strand(fn)],
                     GT_PHASE_CHARS[gt_feature_node_get_phase(fn)]);
}