C++ (Cpp) gt_encseq_builder_enable_description_support示例

示例#1

文件： encseq_lua.c 项目： kowsky/genometools

static int encseq_builder_lua_enable_description_support(lua_State *L)
{
  GtEncseqBuilder **builder;
  builder = check_encseq_builder(L, 1);
  gt_assert(*builder);
  gt_encseq_builder_enable_description_support(*builder);
  return 0;
}

示例#2

文件： shu-encseq-gc.c 项目： 9beckert/TIR

int gt_encseq_gc_unit_test(GtError *err)
{
  int had_err = 0;
  double *results;
  GtEncseqBuilder *eb;
  GtEncseq *encseq;
  const char testseq1[] = "aaaaaa",
             testseq2[] = "cccccc",
             testseq3[] = "acgtacgt",
             testseq4[] = "acgtn";
          /* testseq5[] = "xxxxn"; */
  GtAlphabet *alpha;
/*GtError *tmp_err;*/

  gt_error_check(err);

  alpha = gt_alphabet_new_dna();

  /* test a-seq */
  eb = gt_encseq_builder_new(alpha);
  gt_encseq_builder_create_ssp_tab(eb);
  gt_encseq_builder_enable_description_support(eb);
  gt_encseq_builder_add_cstr(eb, testseq1, 6UL, "only a");
  encseq = gt_encseq_builder_build(eb, err);
  if ((results = gt_encseq_get_gc(encseq,
                                  false,
                                  true,
                                  err)) != NULL)
  {
    gt_ensure(had_err, gt_double_equals_double(results[0], 0.0));
  }
  else
  {
    had_err = -1;
  }
  gt_free(results);
  gt_encseq_builder_delete(eb);
  gt_encseq_delete(encseq);

  if (!had_err)
  {
    /* test c-seq */
    eb = gt_encseq_builder_new(alpha);
    gt_encseq_builder_create_ssp_tab(eb);
    gt_encseq_builder_enable_description_support(eb);
    gt_encseq_builder_add_cstr(eb, testseq2, 6UL, "only c");
    encseq = gt_encseq_builder_build(eb, err);
    if ((results = gt_encseq_get_gc(encseq,
                                    false,
                                    true,
                                    err)) != NULL)
    {
      gt_ensure(had_err, gt_double_equals_one(results[0]));
    }
    else
    {
      had_err = -1;
    }
    gt_free(results);
    gt_encseq_builder_delete(eb);
    gt_encseq_delete(encseq);
  }

  if (!had_err)
  {
    /* test dna-seq and dna+special-seq*/
    eb = gt_encseq_builder_new(alpha);
    gt_encseq_builder_create_ssp_tab(eb);
    gt_encseq_builder_enable_description_support(eb);
    gt_encseq_builder_add_cstr(eb, testseq3, 8UL, "0.5");
    gt_encseq_builder_add_cstr(eb, testseq4, 5UL, "0.5+special");
    encseq = gt_encseq_builder_build(eb, err);
    if ((results = gt_encseq_get_gc(encseq,
                                    false,
                                    true,
                                    err)) != NULL)
    {
      gt_ensure(had_err, gt_double_equals_double(results[0], 0.5));
      gt_ensure(had_err, gt_double_equals_double(results[1], 0.5));
    }
    else
    {
      had_err = -1;
    }
    gt_free(results);

    if (!had_err)
    {
      /* count special chars */
      if ((results = gt_encseq_get_gc(encseq,
                                      true,
                                      true,
                                      err)) != NULL)
      {
        gt_ensure(had_err, gt_double_equals_double(results[0], 0.5));
        gt_ensure(had_err, gt_double_equals_double(results[1], (2.0/5.0)));
      }
      else
      {
        had_err = -1;
      }
      gt_free(results);
    }

    gt_encseq_builder_delete(eb);
    gt_encseq_delete(encseq);
  }

  if (!had_err)
    {
      /* test dna-seq and dna+special-seq*/
      eb = gt_encseq_builder_new(alpha);
      gt_encseq_builder_create_ssp_tab(eb);
      gt_encseq_builder_enable_description_support(eb);
      gt_encseq_builder_add_cstr(eb, testseq3, 8UL, "0.5");
      gt_encseq_builder_add_cstr(eb, testseq4, 5UL, "0.5+special");
      encseq = gt_encseq_builder_build(eb, err);
      /*add mirrored sequence*/
      had_err = gt_encseq_mirror(encseq, err);
      /* sequence wise */
      if ((results = gt_encseq_get_gc(encseq,
                                      false,
                                      true,
                                      err)) != NULL)
      {
        gt_ensure(had_err, gt_double_equals_double(results[0], 0.5));
        gt_ensure(had_err, gt_double_equals_double(results[1], 0.5));
        gt_ensure(had_err, gt_double_equals_double(results[2], 0.5));
        gt_ensure(had_err, gt_double_equals_double(results[3], 0.5));
      }
      else
      {
        had_err = -1;
      }
      gt_free(results);

      if (!had_err)
      {
        /* count special chars */
        if ((results = gt_encseq_get_gc(encseq,
                                        true,
                                        true,
                                        err)) != NULL)
        {
          gt_ensure(had_err, gt_double_equals_double(results[0], 0.5));
          gt_ensure(had_err, gt_double_equals_double(results[1], (2.0/5.0)));
          gt_ensure(had_err, gt_double_equals_double(results[2], (2.0/5.0)));
          gt_ensure(had_err, gt_double_equals_double(results[3], 0.5));
        }
        else
        {
          had_err = -1;
        }
        gt_free(results);
      }
      gt_encseq_builder_delete(eb);
      gt_encseq_delete(encseq);
    }
    gt_alphabet_delete(alpha);
  return had_err;
}