Example #1
0
void gt_rbtree_delete(GtRBTree *tree)
{
  gt_rbtree_clear(tree);
  gt_free(tree);
}
static int hmmsearch_process_coarse_hits(
                                       char *table_filename,
                                       GtCondenseq *ces,
                                       GtCondenseqHmmsearchArguments *arguments,
                                       GtLogger *logger,
                                       GtError *err) {
  int had_err = 0;
  GtStr *line = gt_str_new();
  FILE *table = NULL;
  GtSplitter *splitter = gt_splitter_new();
  GtStr *query = gt_str_new(),
        *fine_fasta_filename = gt_str_new_cstr("condenseq");
  GtRBTree *sequences = NULL;
  GtUword filecount = (GtUword) 1;
  unsigned int querycount = 0;
  const GtUword fine_fasta_name_length = gt_str_length(fine_fasta_filename);
  const GtUword table_name_length = gt_str_length(arguments->outtable_filename);

  table = gt_xfopen(table_filename, "r");

  sequences = gt_rbtree_new(hmmsearch_cmp_seqnum,
                            hmmsearch_tree_free_node, NULL);

  while (!had_err && gt_str_read_next_line(line, table) == 0) {
    char *c_line = gt_str_get(line);
    GtUword uid;
    const GtUword target_column = 0,
          query_column = (GtUword) 3;

    if (c_line[0] != '#') {
      gt_splitter_split_non_empty(splitter, c_line, gt_str_length(line), ' ');
      gt_assert(gt_splitter_size(splitter) == (GtUword) 23);
      if (sscanf(gt_splitter_get_token(splitter, target_column),
                 GT_WU, &uid) != 1) {
        gt_error_set(err, "couldn't parse target number: %s",
                     gt_splitter_get_token(splitter, target_column));
        had_err = -1;
      }
      if (gt_str_length(query) == 0 ||
          strcmp(gt_str_get(query),
                 gt_splitter_get_token(splitter, query_column)) != 0) {
        gt_str_set(query, gt_splitter_get_token(splitter, query_column));
        gt_logger_log(logger, "new query: %s", gt_str_get(query));
        querycount++;
      }
      if (!had_err && querycount == arguments->max_queries) {
        hmmsearch_create_fine_fas(fine_fasta_filename, sequences, ces);
        if (table_name_length != 0)
          gt_str_append_uword(arguments->outtable_filename, filecount++);
        had_err =
          hmmsearch_call_fine_search(table_name_length != 0 ?
                                       arguments->outtable_filename :
                                       NULL,
                                     gt_str_get(fine_fasta_filename),
                                     gt_str_get(arguments->hmmsearch_path),
                                     gt_str_get(arguments->hmm),
                                     logger, err);
        gt_rbtree_clear(sequences);
        gt_str_set_length(fine_fasta_filename, fine_fasta_name_length);
        if (table_name_length != 0)
          gt_str_set_length(arguments->outtable_filename, table_name_length);
        querycount = 0;
      }
      if (!had_err) {
        if (gt_condenseq_each_redundant_seq(ces, uid,
                                            hmmsearch_process_seq,
                                            sequences, err) == 0) {
          had_err = -1;
        }
      }
      gt_splitter_reset(splitter);
    }
    gt_str_reset(line);
  }
  gt_splitter_delete(splitter);
  gt_str_delete(line);
  gt_str_delete(query);
  gt_xfclose(table);

  if (!had_err) {
    hmmsearch_create_fine_fas(fine_fasta_filename, sequences, ces);
    if (table_name_length != 0)
      gt_str_append_uword(arguments->outtable_filename, filecount++);
    had_err =
      hmmsearch_call_fine_search(table_name_length != 0 ?
                                 arguments->outtable_filename :
                                 NULL,
                                 gt_str_get(fine_fasta_filename),
                                 gt_str_get(arguments->hmmsearch_path),
                                 gt_str_get(arguments->hmm),
                                 logger, err);
  }
  gt_log_log("created " GT_WU " files", filecount);
  gt_rbtree_delete(sequences);
  gt_str_delete(fine_fasta_filename);
  return had_err;
}