static int feature_node_lua_new(lua_State *L)
{
GtGenomeNode **gf;
GtUword startpos, endpos;
GtStrand strand;
const char *seqid, *type, *strand_str;
size_t length;
GtStr *seqid_str;
gt_assert(L);
/* get/check parameters */
seqid = luaL_checkstring(L, 1);
type = luaL_checkstring(L, 2);
startpos = luaL_checklong(L, 3);
endpos = luaL_checklong(L, 4);
luaL_argcheck(L, startpos > 0, 3, "must be > 0");
luaL_argcheck(L, endpos > 0, 4, "must be > 0");
luaL_argcheck(L, startpos <= endpos, 3, "must be <= endpos");
strand_str = luaL_checklstring(L, 5, &length);
luaL_argcheck(L, length == 1, 5, "strand string must have length 1");
luaL_argcheck(L, (strand = gt_strand_get(strand_str[0])) !=
GT_NUM_OF_STRAND_TYPES, 5, "invalid strand");
/* construct object */
gf = lua_newuserdata(L, sizeof (GtGenomeNode*));
seqid_str = gt_str_new_cstr(seqid);
*gf = gt_feature_node_new(seqid_str, type, startpos, endpos, strand);
gt_str_delete(seqid_str);
gt_assert(*gf);
luaL_getmetatable(L, GENOME_NODE_METATABLE);
lua_setmetatable(L, -2);
return 1;
}
static int gt_ltrdigest_pdom_visitor_parse_query(GtLTRdigestPdomVisitor *lv,
GtHMMERParseStatus *status,
bool *end,
FILE *instream, GtError *err)
{
int had_err = 0;
char buf[GT_HMMER_BUF_LEN];
gt_assert(lv && instream && status);
gt_error_check(err);
had_err = pdom_parser_get_next_line(buf, instream, err);
if (!had_err && strncmp("Query:", buf, (size_t) 6) != 0) {
*end = true;
}
if (!had_err && !(*end)) {
status->strand = gt_strand_get(buf[14]);
buf[14] = '\0';
status->frame = (unsigned) atoi(buf+13);
}
if (!had_err && !(*end)) {
had_err = gt_ltrdigest_pdom_visitor_parse_scores(lv, buf, instream, err);
}
if (!had_err && !(*end)) {
had_err = gt_ltrdigest_pdom_visitor_parse_domainhits(lv, status, buf,
instream, err);
}
if (!had_err && !(*end)) {
had_err = gt_ltrdigest_pdom_visitor_parse_statistics(lv, buf, instream,
err);
}
return had_err;
}
static int process_gt_strand_arg(GtStr *gt_strand_char, GtStrand *strand,
const char *optstr, GtError *err)
{
int had_err = 0;
gt_error_check(err);
if (gt_str_length(gt_strand_char)) {
GtStrand tmpstrand = gt_strand_get(gt_str_get(gt_strand_char)[0]);
if ((gt_str_length(gt_strand_char) > 1) ||
(tmpstrand == GT_NUM_OF_STRAND_TYPES)) {
gt_error_set(err, "argument to option -%s must be one of '"
GT_STRAND_CHARS"'", optstr);
had_err = -1;
}
if (!had_err)
*strand = tmpstrand;
}
return had_err;
}
int gt_parse_strand(GtStrand *gt_strand_value, const char *strand,
unsigned int line_number, const char *filename,
GtError *err)
{
gt_assert(strand && filename);
gt_error_check(err);
if (strlen(strand) != 1) {
gt_error_set(err, "strand '%s' not one character long on line %u in file "
"'%s'", strand, line_number, filename);
*gt_strand_value = GT_STRAND_UNKNOWN;
return -1;
}
if (strspn(strand, GT_STRAND_CHARS) != 1) {
gt_error_set(err, "strand '%s' on line %u in file '%s' not a valid "
"character from the set '%s'", strand, line_number, filename,
GT_STRAND_CHARS);
*gt_strand_value = GT_STRAND_UNKNOWN;
return -1;
}
*gt_strand_value = gt_strand_get(strand[0]);
return 0;
}
