C++ (Cpp) gt_feature_index_get_features_for_seqid Examples

Example #1

static int feature_index_lua_get_features_for_seqid(lua_State *L)
{
  GtFeatureIndex **feature_index;
  const char *seqid;
  GtArray *features;
  feature_index = check_feature_index(L, 1);
  seqid = luaL_checkstring(L, 2);
  features = gt_feature_index_get_features_for_seqid(*feature_index, seqid);
  push_features_as_table(L, features);
  gt_array_delete(features);
  return 1;
}

Example #2

File: feature_in_stream.c Project: lparsons/genometools

static int feature_in_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
                                   GtError *error)
{
  GtFeatureInStream *stream = feature_in_stream_cast(ns);
  gt_error_check(error);

  if (!stream->init)
  {
    feature_in_stream_init(stream);
    stream->init = true;
  }

  if (gt_queue_size(stream->regioncache) > 0)
  {
    GtGenomeNode *region = gt_queue_get(stream->regioncache);
    *gn = region;
    return 0;
  }

  if (stream->featurecache == NULL || gt_array_size(stream->featurecache) == 0)
  {
    if (stream->featurecache != NULL)
    {
      gt_array_delete(stream->featurecache);
      stream->featurecache = NULL;
    }

    if (stream->seqindex == gt_str_array_size(stream->seqids))
    {
      *gn = NULL;
      return 0;
    }

    const char *seqid = gt_str_array_get(stream->seqids, stream->seqindex++);
    stream->featurecache = gt_feature_index_get_features_for_seqid(stream->fi,
                                                                   seqid,
                                                                   error);
    gt_array_sort(stream->featurecache, (GtCompare)gt_genome_node_compare);
    gt_array_reverse(stream->featurecache);
  }

  GtGenomeNode *feat = *(GtGenomeNode **)gt_array_pop(stream->featurecache);
  *gn = gt_genome_node_ref(feat);
  return 0;
}

Example #3

File: feature_index_lua.c Project: AlexWoroschilow/uni_hamburg

static int feature_index_lua_get_features_for_seqid(lua_State *L)
{
  GtFeatureIndex **feature_index;
  const char *seqid;
  GtArray *features;
  GtError *err;
  feature_index = check_feature_index(L, 1);
  seqid = luaL_checkstring(L, 2);
  err = gt_error_new();
  features = gt_feature_index_get_features_for_seqid(*feature_index, seqid,
                                                     err);
  if (!features)
    return gt_lua_error(L, err);
  gt_error_delete(err);
  push_features_as_table(L, features);
  gt_array_delete(features);
  return 1;
}