static int feature_node_lua_remove_leaf(lua_State *L)
{
GtGenomeNode **parent, **leaf;
GtFeatureNode *pf, *lf;
parent = check_genome_node(L, 1);
leaf = check_genome_node(L, 2);
pf = gt_feature_node_try_cast(*parent);
luaL_argcheck(L, pf, 1, "not a feature node");
lf = gt_feature_node_try_cast(*leaf);
luaL_argcheck(L, lf, 2, "not a feature node");
gt_feature_node_remove_leaf(pf, lf);
return 0;
}
static int genome_node_lua_add_child(lua_State *L)
{
GtGenomeNode **parent, **child;
GtFeatureNode *pf, *cf;
parent = check_genome_node(L, 1);
child = check_genome_node(L, 2);
pf = gt_feature_node_try_cast(*parent);
luaL_argcheck(L, pf, 1, "not a feature node");
cf = gt_feature_node_try_cast(*child);
luaL_argcheck(L, cf, 2, "not a feature node");
gt_feature_node_add_child(pf, (GtFeatureNode*)
gt_genome_node_ref((GtGenomeNode*) cf));
return 0;
}
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;
}
static int lua_custom_visitor_visit_node_generic(GT_UNUSED GtNodeVisitor *nv,
GtGenomeNode *fn,
const char *function,
GtError *err)
{
GT_UNUSED GtNodeVisitor **vis;
GtLuaCustomVisitor *lcv;
GT_UNUSED GtGenomeNode **node;
int had_err = 0;
gt_assert(nv);
lcv = lua_custom_visitor_cast(nv);
node = check_genome_node(lcv->L, 1);
vis = check_genome_visitor(lcv->L, 2);
gt_assert(*node == (GtGenomeNode*) fn);
gt_assert(*vis == (GtNodeVisitor*) nv);
lua_pushvalue(lcv->L, 2);
lua_pushstring(lcv->L, function);
lua_gettable(lcv->L, 2);
if (lua_isnil(lcv->L, -1)) {
lua_pop(lcv->L, 1);
return had_err;
}
lua_pushvalue(lcv->L, 2);
gt_lua_genome_node_push(lcv->L, gt_genome_node_ref((GtGenomeNode*) fn));
if (lua_pcall(lcv->L, 2, 0, 0)) {
const char *error = lua_tostring(lcv->L, -1);
gt_error_set(err, "%s", error);
had_err = -1;
}
return had_err;
}
static int feature_node_lua_extract_sequence(lua_State *L)
{
GtGenomeNode **gn;
GtFeatureNode *fn;
const char *type;
bool join;
GtRegionMapping **region_mapping;
GtStr *sequence;
GtError *err;
gn = check_genome_node(L, 1);
/* make sure we get a feature node */
fn = gt_feature_node_try_cast(*gn);
luaL_argcheck(L, fn, 1, "not a feature node");
type = luaL_checkstring(L, 2);
join = lua_toboolean(L, 3);
region_mapping = check_region_mapping(L, 4);
err = gt_error_new();
sequence = gt_str_new();
if (gt_extract_feature_sequence(sequence, *gn, type, join, NULL, NULL,
*region_mapping, err)) {
gt_str_delete(sequence);
return gt_lua_error(L, err);
}
if (gt_str_length(sequence))
lua_pushstring(L, gt_str_get(sequence));
else
lua_pushnil(L);
gt_str_delete(sequence);
gt_error_delete(err);
return 1;
}
static int genome_node_lua_delete(lua_State *L)
{
GtGenomeNode **gn;
gn = check_genome_node(L, 1);
gt_genome_node_delete(*gn);
return 0;
}
static int genome_node_lua_contains_marked(lua_State *L)
{
GtGenomeNode **gn;
gn = check_genome_node(L, 1);
lua_pushboolean(L,
gt_feature_node_contains_marked(gt_feature_node_cast(*gn)));
return 1;
}
static int genome_node_lua_get_seqid(lua_State *L)
{
GtStr *seqid;
GtGenomeNode **gn = check_genome_node(L, 1);
if ((seqid = gt_genome_node_get_seqid(*gn)))
lua_pushstring(L, gt_str_get(seqid));
else
lua_pushnil(L);
return 1;
}
static int feature_node_lua_get_source(lua_State *L)
{
GtGenomeNode **gn = check_genome_node(L, 1);
GtFeatureNode *fn;
/* make sure we get a feature node */
fn = gt_feature_node_try_cast(*gn);
luaL_argcheck(L, fn, 1, "not a feature node");
lua_pushstring(L, gt_feature_node_get_source(fn));
return 1;
}
static int feature_node_lua_output_leading(lua_State *L)
{
GtGenomeNode **gn;
GtFeatureNode *fn;
gn = check_genome_node(L, 1);
/* make sure we get a feature node */
fn = gt_feature_node_try_cast(*gn);
luaL_argcheck(L, fn, 1, "not a feature node");
gt_gff3_output_leading(fn, NULL);
return 0;
}
static int feature_node_iterator_lua_new_direct(lua_State *L)
{
GtFeatureNodeIterator **fni;
GtFeatureNode **fn;
gt_assert(L);
fn = (GtFeatureNode**) check_genome_node(L, 1);
fni = lua_newuserdata(L, sizeof (GtFeatureNodeIterator*));
gt_assert(fni);
*fni = gt_feature_node_iterator_new_direct(*fn);
luaL_getmetatable(L, GENOME_NODE_ITERATOR_METATABLE);
lua_setmetatable(L, -2);
return 1;
}
static int genome_node_lua_accept(lua_State *L)
{
GtGenomeNode **gn;
GtNodeVisitor **gv;
GtError *err;
gn = check_genome_node(L, 1);
gv = check_genome_visitor(L, 2);
err = gt_error_new();
if (gt_genome_node_accept(*gn, *gv, err))
return gt_lua_error(L, err);
gt_error_delete(err);
return 0;
}
static int feature_node_lua_get_score(lua_State *L)
{
GtGenomeNode **gn = check_genome_node(L, 1);
GtFeatureNode *fn;
/* make sure we get a feature node */
fn = gt_feature_node_try_cast(*gn);
luaL_argcheck(L, fn, 1, "not a feature node");
if (gt_feature_node_score_is_defined(fn))
lua_pushnumber(L, gt_feature_node_get_score(fn));
else
lua_pushnil(L);
return 1;
}
static int feature_node_lua_get_strand(lua_State *L)
{
GtGenomeNode **gn = check_genome_node(L, 1);
GtFeatureNode *fn;
char strand_char[2];
/* make sure we get a feature node */
fn = gt_feature_node_try_cast(*gn);
luaL_argcheck(L, fn, 1, "not a feature node");
strand_char[0] = GT_STRAND_CHARS[gt_feature_node_get_strand(fn)];
strand_char[1] = '\0';
lua_pushstring(L, strand_char);
return 1;
}
static int feature_index_lua_add_region_node(lua_State *L)
{
GtFeatureIndex **fi;
GtGenomeNode **gn;
GtRegionNode *rn;
gt_assert(L);
fi = check_feature_index(L, 1);
gn = check_genome_node(L, 2);
rn = gt_region_node_try_cast(*gn);
luaL_argcheck(L, rn, 2, "not a region node");
gt_feature_index_add_region_node(*fi, rn);
return 0;
}
static int feature_node_lua_set_source(lua_State *L)
{
const char *source;
GtStr *source_str;
GtGenomeNode **gn = check_genome_node(L, 1);
GtFeatureNode *fn;
/* make sure we get a feature node */
fn = gt_feature_node_try_cast(*gn);
luaL_argcheck(L, fn, 1, "not a feature node");
source = luaL_checkstring(L, 2);
source_str = gt_str_new_cstr(source);
gt_feature_node_set_source(fn, source_str);
gt_str_delete(source_str);
return 0;
}
static int feature_node_lua_get_attribute(lua_State *L)
{
GtGenomeNode **gn = check_genome_node(L, 1);
const char *attr = NULL, *attrval = NULL;
attr = luaL_checkstring(L, 2);
GtFeatureNode *fn;
/* make sure we get a feature node */
fn = gt_feature_node_try_cast(*gn);
luaL_argcheck(L, fn, 1, "not a feature node");
attrval = gt_feature_node_get_attribute(fn, attr);
if (attrval)
lua_pushstring(L, attrval);
else
lua_pushnil(L);
return 1;
}
static int feature_index_lua_add_region_node(lua_State *L)
{
GtFeatureIndex **fi;
GtGenomeNode **gn;
GtRegionNode *rn;
GtError *err;
gt_assert(L);
fi = check_feature_index(L, 1);
gn = check_genome_node(L, 2);
rn = gt_region_node_try_cast(*gn);
luaL_argcheck(L, rn, 2, "not a region node");
err = gt_error_new();
if (gt_feature_index_add_region_node(*fi, rn, err))
return gt_lua_error(L, err);
gt_error_delete(err);
return 0;
}
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;
}
static int feature_node_lua_get_exons(lua_State *L)
{
GtGenomeNode **gn = check_genome_node(L, 1);
GtArray *exons = gt_array_new(sizeof (GtGenomeNode*));
GtUword i = 0;
GtFeatureNode *fn;
/* make sure we get a feature node */
fn = gt_feature_node_try_cast(*gn);
luaL_argcheck(L, fn, 1, "not a feature node");
gt_feature_node_get_exons(fn, exons);
lua_newtable(L);
for (i = 0; i < gt_array_size(exons); i++) {
lua_pushnumber(L, i+1);
gt_lua_genome_node_push(L, (GtGenomeNode*)
gt_genome_node_ref(*(GtGenomeNode**)
gt_array_get(exons, i)));
lua_rawset(L, -3);
}
gt_array_delete(exons);
return 1;
}
static int genome_node_lua_get_range(lua_State *L)
{
GtGenomeNode **gn = check_genome_node(L, 1);
return gt_lua_range_push(L, gt_genome_node_get_range(*gn));
}
static int genome_node_lua_get_filename(lua_State *L)
{
GtGenomeNode **gn = check_genome_node(L, 1);
lua_pushstring(L, gt_genome_node_get_filename(*gn));
return 1;
}
static int genome_node_lua_mark(lua_State *L)
{
GtGenomeNode **gn = check_genome_node(L, 1);
gt_feature_node_mark(gt_feature_node_cast(*gn));
return 0;
}
