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 feature_index_lua_get_features_for_range(lua_State *L)
{
GtFeatureIndex **feature_index;
const char *seqid;
GtRange *range;
GtError *err;
bool has_seqid;
GtArray *features;
GT_UNUSED int had_err;
feature_index = check_feature_index(L, 1);
seqid = luaL_checkstring(L, 2);
err = gt_error_new();
if (gt_feature_index_has_seqid(*feature_index, &has_seqid, seqid, err))
return gt_lua_error(L, err);
gt_error_delete(err);
luaL_argcheck(L, has_seqid, 2,
"feature_index does not contain seqid");
range = check_range(L, 3);
features = gt_array_new(sizeof (GtGenomeNode*));
err = gt_error_new();
had_err = gt_feature_index_get_features_for_range(*feature_index, features,
seqid, range, err);
if (had_err)
return gt_lua_error(L, err);
gt_error_delete(err);
push_features_as_table(L, features);
gt_array_delete(features);
return 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;
}
static int feature_visitor_lua_new(lua_State *L)
{
GtNodeVisitor **feature_visitor;
GtFeatureIndex **feature_index;
feature_visitor = lua_newuserdata(L, sizeof (GtNodeVisitor*));
gt_assert(feature_visitor);
feature_index = check_feature_index(L, 1);
*feature_visitor = gt_feature_visitor_new(*feature_index);
luaL_getmetatable(L, GENOME_VISITOR_METATABLE);
lua_setmetatable(L, -2);
return 1;
}
static int feature_index_lua_get_range_for_seqid(lua_State *L)
{
GtFeatureIndex **feature_index;
const char *seqid;
GtRange range;
feature_index = check_feature_index(L, 1);
seqid = luaL_checkstring(L, 2);
luaL_argcheck(L, gt_feature_index_has_seqid(*feature_index, seqid), 2,
"feature_index does not contain seqid");
gt_feature_index_get_range_for_seqid(*feature_index, &range, seqid);
return gt_lua_range_push(L, range);
}
static int feature_index_lua_get_first_seqid(lua_State *L)
{
GtFeatureIndex **feature_index;
const char *seqid;
feature_index = check_feature_index(L, 1);
seqid = gt_feature_index_get_first_seqid(*feature_index);
if (seqid)
lua_pushstring(L, seqid);
else
lua_pushnil(L);
return 1;
}
static int feature_index_lua_get_seqids(lua_State *L)
{
GtFeatureIndex **feature_index;
GtStrArray *seqids;
feature_index = check_feature_index(L, 1);
seqids = gt_feature_index_get_seqids(*feature_index);
gt_assert(seqids);
/* push table containing sequence ids onto the stack */
gt_lua_push_strarray_as_table(L, seqids);
gt_str_array_delete(seqids);
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_index_lua_add_gff3file(lua_State *L)
{
GtFeatureIndex **fi;
const char *filename;
GtError *err;
gt_assert(L);
fi = check_feature_index(L, 1);
filename = luaL_checkstring(L, 2);
err = gt_error_new();
if (gt_feature_index_add_gff3file(*fi, filename, err))
return gt_lua_error(L, err);
gt_error_delete(err);
return 0;
}
static int feature_index_lua_get_seqids(lua_State *L)
{
GtFeatureIndex **feature_index;
GtStrArray *seqids;
GtError *err;
feature_index = check_feature_index(L, 1);
err = gt_error_new();
seqids = gt_feature_index_get_seqids(*feature_index, err);
if (!seqids)
return gt_lua_error(L, err);
gt_error_delete(err);
/* push table containing sequence ids onto the stack */
gt_lua_push_strarray_as_table(L, seqids);
gt_str_array_delete(seqids);
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_has_seqid(lua_State *L)
{
GtFeatureIndex **feature_index;
bool has_seqid;
const char *seqid;
GtError *err;
int had_err = 0;
feature_index = check_feature_index(L, 1);
seqid = luaL_checkstring(L, 2);
err = gt_error_new();
had_err = gt_feature_index_has_seqid(*feature_index, &has_seqid, seqid, err);
if (had_err)
return gt_lua_error(L, err);
gt_error_delete(err);
lua_pushboolean(L, has_seqid);
return 1;
}
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_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;
}
static int feature_index_lua_get_first_seqid(lua_State *L)
{
GtFeatureIndex **feature_index;
char *seqid;
GtError *err;
feature_index = check_feature_index(L, 1);
err = gt_error_new();
seqid = gt_feature_index_get_first_seqid(*feature_index, err);
if (gt_error_is_set(err))
return gt_lua_error(L, err);
gt_error_delete(err);
if (seqid) {
lua_pushstring(L, seqid);
gt_free(seqid);
} else
lua_pushnil(L);
return 1;
}
static int feature_index_lua_get_features_for_range(lua_State *L)
{
GtFeatureIndex **feature_index;
const char *seqid;
GtRange *range;
GtArray *features;
int had_err;
feature_index = check_feature_index(L, 1);
seqid = luaL_checkstring(L, 2);
luaL_argcheck(L, gt_feature_index_has_seqid(*feature_index, seqid), 2,
"feature_index does not contain seqid");
range = check_range(L, 3);
features = gt_array_new(sizeof (GtGenomeNode*));
had_err = gt_feature_index_get_features_for_range(*feature_index, features,
seqid, range, NULL);
gt_assert(!had_err); /* it was checked before that the feature_index contains
the given sequence id*/
push_features_as_table(L, features);
gt_array_delete(features);
return 1;
}
static int feature_index_lua_get_range_for_seqid(lua_State *L)
{
GtFeatureIndex **feature_index;
const char *seqid;
GtError *err;
GtRange range;
bool has_seqid;
feature_index = check_feature_index(L, 1);
seqid = luaL_checkstring(L, 2);
err = gt_error_new();
if (gt_feature_index_has_seqid(*feature_index, &has_seqid, seqid, err))
return gt_lua_error(L, err);
gt_error_delete(err);
luaL_argcheck(L, has_seqid, 2,
"feature_index does not contain seqid");
err = gt_error_new();
if (gt_feature_index_get_range_for_seqid(*feature_index, &range, seqid, err))
return gt_lua_error(L, err);
gt_error_delete(err);
return gt_lua_range_push(L, range);
}
static int feature_index_lua_delete(lua_State *L)
{
GtFeatureIndex **feature_index = check_feature_index(L, 1);
gt_feature_index_delete(*feature_index);
return 0;
}
