C++ (Cpp) gt_feature_index_add_feature_node Exemples

Exemple #1

Fichier : feature_index_lua.c Projet : AlexWoroschilow/uni_hamburg

static int feature_index_lua_add_feature_node(lua_State *L)
{
  GtFeatureIndex **fi;
  GtGenomeNode **gn;
  GtFeatureNode *fn;
  GtStr *seqid;
  GtError *err;
  bool has_seqid;
  gt_assert(L);
  fi = check_feature_index(L, 1);
  gn = check_genome_node(L, 2);
  fn = gt_feature_node_cast(*gn);
  luaL_argcheck(L, fn, 2, "not a feature node");
  seqid = gt_genome_node_get_seqid(*gn);
  luaL_argcheck(L, seqid, 2, "feature does not have a sequence id");
  err = gt_error_new();
  if (gt_feature_index_has_seqid(*fi, &has_seqid, gt_str_get(seqid), err))
    return gt_lua_error(L, err);
  gt_error_delete(err);
  luaL_argcheck(L, has_seqid, 2,
                "feature index does not contain corresponding sequence region");
  err = gt_error_new();
  if (gt_feature_index_add_feature_node(*fi, fn, err))
    return gt_lua_error(L, err);
  gt_error_delete(err);
  return 0;
}

Exemple #2

Fichier : diagram.c Projet : AlexWoroschilow/uni_hamburg

int gt_diagram_unit_test(GtError *err)
{
  int had_err = 0;
  GtGenomeNode *gn;
  GtDiagramTestShared sh;
  GtRange testrng = {100, 10000};
  gt_error_check(err);

  gn = gt_feature_node_new_standard_gene();
  sh.fi = gt_feature_index_memory_new();
  sh.sty = gt_style_new(err);
  sh.err = err;
  sh.errstatus = 0;
  gt_feature_index_add_feature_node(sh.fi, gt_feature_node_cast(gn), err);
  gt_genome_node_delete(gn);
  sh.d = gt_diagram_new(sh.fi, "ctg123", &testrng, sh.sty, err);

  /* removed the multithreading test for now until it is fixed */
  gt_diagram_unit_test_sketch_func(&sh);
  gt_ensure(sh.errstatus == 0);

  gt_style_delete(sh.sty);
  gt_diagram_delete(sh.d);
  gt_feature_index_delete(sh.fi);

  return had_err;
}

Exemple #3

Fichier : feature_in_stream.c Projet : lparsons/genometools

static GtFeatureIndex *in_stream_test_data(GtError *error)
{
  GtFeatureIndex *fi;
  GtFeatureNode *fn;
  GtGenomeNode *gn;
  GtRegionNode *rn;
  GtStr *seqid;

  fi = gt_feature_index_memory_new();

  seqid = gt_str_new_cstr("chr1");
  gn = gt_region_node_new(seqid, 1, 100000);
  rn = gt_region_node_cast(gn);
  gt_feature_index_add_region_node(fi, rn, error);
  gt_genome_node_delete(gn);

  gn = gt_feature_node_new(seqid, "region", 500, 5000, GT_STRAND_BOTH);
  fn = gt_feature_node_cast(gn);
  gt_feature_index_add_feature_node(fi, fn, error);
  gt_genome_node_delete(gn);

  gn = gt_feature_node_new(seqid, "region", 50000, 75000, GT_STRAND_BOTH);
  fn = gt_feature_node_cast(gn);
  gt_feature_index_add_feature_node(fi, fn, error);
  gt_genome_node_delete(gn);

  gt_str_delete(seqid);
  seqid = gt_str_new_cstr("scf0001");
  gn = gt_region_node_new(seqid, 1, 10000);
  rn = gt_region_node_cast(gn);
  gt_feature_index_add_region_node(fi, rn, error);
  gt_genome_node_delete(gn);

  gn = gt_feature_node_new(seqid, "mRNA", 4000, 6000, GT_STRAND_REVERSE);
  fn = gt_feature_node_cast(gn);
  gt_feature_index_add_feature_node(fi, fn, error);
  gt_genome_node_delete(gn);

  gn = gt_feature_node_new(seqid, "mRNA", 7000, 9500, GT_STRAND_FORWARD);
  fn = gt_feature_node_cast(gn);
  gt_feature_index_add_feature_node(fi, fn, error);
  gt_genome_node_delete(gn);

  gt_str_delete(seqid);

  return fi;
}

Exemple #4

Fichier : feature_visitor.c Projet : simongog/genometools

static int feature_visitor_feature_node(GtNodeVisitor *gv, GtFeatureNode *fn,
                                        GtError *err)
{
  GtFeatureVisitor *v = feature_visitor_cast(gv);
  int rval = 0;
  gt_error_check(err);
  rval = gt_feature_index_add_feature_node(v->feature_index, fn, err);
  return rval;
}

Exemple #5

static int feature_index_lua_add_feature_node(lua_State *L)
{
  GtFeatureIndex **fi;
  GtGenomeNode **gn;
  GtFeatureNode *gf;
  GtStr *seqid;
  gt_assert(L);
  fi = check_feature_index(L, 1);
  gn = check_genome_node(L, 2);
  gf = gt_genome_node_cast(gt_feature_node_class(), *gn);
  luaL_argcheck(L, gf, 2, "not a feature node");
  seqid = gt_genome_node_get_seqid(*gn);
  luaL_argcheck(L, seqid, 2, "feature does not have a sequence id");
  luaL_argcheck(L, gt_feature_index_has_seqid(*fi, gt_str_get(seqid)), 2,
                "feature index does not contain corresponding sequence region");
  gt_feature_index_add_feature_node(*fi, gf);
  return 0;
}

Exemple #6

Fichier : feature_index.c Projet : AlexWoroschilow/uni_hamburg

static void* gt_feature_index_unit_test_add(void *data)
{
  GtFeatureNode *feature;
  GtFeatureIndexTestShared *shm = (GtFeatureIndexTestShared*) data;

  while (true) {
    gt_mutex_lock(shm->mutex);
    if (shm->next_node_idx == GT_FI_TEST_FEATURES_PER_THREAD * gt_jobs) {
      gt_mutex_unlock(shm->mutex);
      return NULL;
    }
    gt_assert(shm->next_node_idx < gt_array_size(shm->nodes));
    feature = *(GtFeatureNode**) gt_array_get(shm->nodes, shm->next_node_idx++);
    gt_mutex_unlock(shm->mutex);
    gt_feature_index_add_feature_node(shm->fi, feature, shm->err);
    gt_genome_node_delete((GtGenomeNode*) feature);
  }
  return NULL;
}