static void targetbest_filter_stream_free(GtNodeStream *gs)
{
GtTargetbestFilterStream *tfs = targetbest_filter_stream_cast(gs);
for (; tfs->next != NULL; tfs->next = gt_dlistelem_next(tfs->next))
gt_genome_node_delete(gt_dlistelem_get_data(tfs->next));
gt_dlist_delete(tfs->trees);
gt_hashmap_delete(tfs->target_to_elem);
gt_node_stream_delete(tfs->in_stream);
}
void *gt_ranked_list_iter_prev(GtRankedListIter *ranked_list_iter)
{
/* return gt_rbtree_iter_next(ranked_list_iter); */
void *data = NULL;
if (ranked_list_iter->current_elem != NULL) {
data = gt_dlistelem_get_data(ranked_list_iter->current_elem);
ranked_list_iter->current_elem =
gt_dlistelem_next(ranked_list_iter->current_elem);
}
return data;
}
GtDlistelem* gt_dlist_find(const GtDlist *dlist, void *new_data)
{
GtDlistelem *dlistelem;
void *old_data;
gt_assert(dlist);
for (dlistelem = gt_dlist_first(dlist); dlistelem != NULL;
dlistelem = gt_dlistelem_next(dlistelem)) {
old_data = gt_dlistelem_get_data(dlistelem);
if (dlist->cmp_func && !dlist->cmp_func(old_data, new_data))
return dlistelem;
else if (old_data == new_data)
return dlistelem;
}
return NULL;
}
void gt_ranked_list_delete(GtRankedList *ranked_list)
{
if (ranked_list == NULL) return;
/* gt_rbtree_delete(ranked_list->root); */
if (ranked_list->free_func != NULL) {
GtDlistelem *dlistelem;
for (dlistelem = gt_dlist_first(ranked_list->list); dlistelem != NULL;
dlistelem = gt_dlistelem_next(dlistelem)) {
void *data = gt_dlistelem_get_data(dlistelem);
ranked_list->free_func(data);
}
}
gt_dlist_delete(ranked_list->list);
gt_free(ranked_list);
}
static void feature_node_free(GtGenomeNode *gn)
{
GtFeatureNode *fn = gt_feature_node_cast(gn);
gt_str_delete(fn->seqid);
gt_str_delete(fn->source);
gt_tag_value_map_delete(fn->attributes);
if (fn->children) {
GtDlistelem *dlistelem;
for (dlistelem = gt_dlist_first(fn->children);
dlistelem != NULL;
dlistelem = gt_dlistelem_next(dlistelem)) {
gt_genome_node_delete(gt_dlistelem_get_data(dlistelem));
}
}
gt_dlist_delete(fn->children);
if (fn->observer && fn->observer->deleted)
fn->observer->deleted(fn, fn->observer->data);
if (fn->observer)
gt_feature_node_observer_delete(fn->observer);
}
static int targetbest_filter_stream_next(GtNodeStream *gs, GtGenomeNode **gn,
GtError *err)
{
GtTargetbestFilterStream *tfs;
GtGenomeNode *node;
int had_err = 0;
gt_error_check(err);
tfs = targetbest_filter_stream_cast(gs);
if (!tfs->in_stream_processed) {
while (!(had_err = gt_node_stream_next(tfs->in_stream, &node, err)) &&
node) {
if (gt_feature_node_try_cast(node) &&
gt_feature_node_get_attribute((GtFeatureNode*) node, "Target")) {
filter_targetbest((GtFeatureNode*) node, tfs->trees,
tfs->target_to_elem);
}
else
gt_dlist_add(tfs->trees, node);
}
tfs->next = gt_dlist_first(tfs->trees);
tfs->in_stream_processed = true;
}
if (!had_err) {
gt_assert(tfs->in_stream_processed);
if (tfs->next) {
*gn = gt_dlistelem_get_data(tfs->next);
tfs->next = gt_dlistelem_next(tfs->next);
}
else
*gn = NULL;
return 0;
}
return had_err;
}
int gt_dlist_example(GT_UNUSED GtError *err)
{
GtDlistelem *dlistelem;
GtDlist *dlist;
void *data;
int elem = 1984;
gt_error_check(err);
dlist = gt_dlist_new(NULL);
gt_dlist_add(dlist, &elem);
gt_dlist_add(dlist, &elem);
gt_dlist_add(dlist, &elem);
/* a typical iterator loop */
for (dlistelem = gt_dlist_first(dlist); dlistelem != NULL;
dlistelem = gt_dlistelem_next(dlistelem)) {
data = gt_dlistelem_get_data(dlistelem);
/* do something with data */
}
gt_dlist_delete(dlist);
return 0;
}
static void gt_aligned_segments_pile_delete_finishing_before(
GtAlignedSegmentsPile *asp, unsigned long position)
{
GtDlistelem *dlistelem, *dlistelem_to_remove = NULL;
for (dlistelem = gt_dlist_first(asp->set); dlistelem != NULL;
dlistelem = gt_dlistelem_next(dlistelem))
{
GtAlignedSegment *as;
if (dlistelem_to_remove != NULL)
{
gt_dlist_remove(asp->set, dlistelem_to_remove);
dlistelem_to_remove = NULL;
}
as = gt_dlistelem_get_data(dlistelem);
if (gt_aligned_segment_refregion_endpos(as) < position)
{
if (asp->process_complete != NULL)
{
asp->process_complete(as, asp->process_complete_data);
}
if (asp->delete_processed_segments)
gt_aligned_segment_delete(as);
/* delay elem removal to avoid disrupting list traversal */
dlistelem_to_remove = dlistelem;
}
else
{
break;
}
}
if (dlistelem_to_remove != NULL)
{
gt_dlist_remove(asp->set, dlistelem_to_remove);
dlistelem_to_remove = NULL;
}
}
int gt_dlist_unit_test(GtError *err)
{
GtDlist *dlist;
GtDlistelem *dlistelem;
int i, j, size, *data,
elem_a = 7,
elem_b = 6,
elems[MAX_SIZE],
elems_backup[MAX_SIZE],
had_err = 0;
gt_error_check(err);
/* boundary case: empty dlist */
dlist = gt_dlist_new(intcompare);
ensure(had_err, !gt_dlist_size(dlist));
gt_dlist_delete(dlist);
dlist = gt_dlist_new(NULL);
ensure(had_err, !gt_dlist_size(dlist));
gt_dlist_delete(dlist);
/* boundary case: dlist containing one element */
dlist = gt_dlist_new(intcompare);
gt_dlist_add(dlist, &elem_a);
ensure(had_err, gt_dlist_size(dlist) == 1);
ensure(had_err,
elem_a == *(int*) gt_dlistelem_get_data(gt_dlist_first(dlist)));
gt_dlist_delete(dlist);
dlist = gt_dlist_new(NULL);
gt_dlist_add(dlist, &elem_a);
ensure(had_err, gt_dlist_size(dlist) == 1);
ensure(had_err,
elem_a == *(int*) gt_dlistelem_get_data(gt_dlist_first(dlist)));
gt_dlist_delete(dlist);
/* boundary case: dlist containing two elements */
dlist = gt_dlist_new(intcompare);
gt_dlist_add(dlist, &elem_a);
gt_dlist_add(dlist, &elem_b);
ensure(had_err, gt_dlist_size(dlist) == 2);
ensure(had_err,
elem_b == *(int*) gt_dlistelem_get_data(gt_dlist_first(dlist)));
gt_dlist_delete(dlist);
dlist = gt_dlist_new(NULL);
gt_dlist_add(dlist, &elem_a);
gt_dlist_add(dlist, &elem_b);
ensure(had_err, gt_dlist_size(dlist) == 2);
ensure(had_err,
elem_a == *(int*) gt_dlistelem_get_data(gt_dlist_first(dlist)));
gt_dlist_delete(dlist);
for (i = 0; i < NUM_OF_TESTS && !had_err; i++) {
/* construct the random elements for the list */
size = gt_rand_max(MAX_SIZE);
for (j = 0; j < size; j++) {
elems[j] = gt_rand_max(INT_MAX);
elems_backup[j] = elems[j];
}
/* sort the backup elements */
qsort(elems_backup, size, sizeof (int), intcompare);
/* test with compare function */
dlist = gt_dlist_new(intcompare);
ensure(had_err, !gt_dlist_size(dlist));
for (j = 0; j < size && !had_err; j++) {
gt_dlist_add(dlist, elems + j);
ensure(had_err, gt_dlist_size(dlist) == j+1);
for (dlistelem = gt_dlist_first(dlist); dlistelem != NULL;
dlistelem = gt_dlistelem_next(dlistelem)) {
}
}
j = 0;
for (dlistelem = gt_dlist_first(dlist); dlistelem != NULL;
dlistelem = gt_dlistelem_next(dlistelem)) {
data = gt_dlistelem_get_data(dlistelem);
ensure(had_err, *data == elems_backup[j]);
j++;
}
/* test gt_dlist_find() */
for (j = 0; j < size; j++) {
dlistelem = gt_dlist_find(dlist, elems_backup + j);
ensure(had_err, dlistelem);
ensure(had_err,
*(int*) gt_dlistelem_get_data(dlistelem) == elems_backup[j]);
}
/* remove first element */
if (gt_dlist_size(dlist)) {
gt_dlist_remove(dlist, gt_dlist_first(dlist));
if (gt_dlist_size(dlist)) {
data = gt_dlistelem_get_data(gt_dlist_first(dlist));
ensure(had_err, *data == elems_backup[1]);
}
}
/* remove last element */
if (gt_dlist_size(dlist)) {
gt_dlist_remove(dlist, gt_dlist_last(dlist));
if (gt_dlist_size(dlist)) {
data = gt_dlistelem_get_data(gt_dlist_last(dlist));
ensure(had_err, *data == elems_backup[size - 2]);
}
}
/* XXX: fix this */
#if 0
/* remove middle element */
if (gt_dlist_size(dlist) >= 2) {
dlistelem = gt_dlist_first(dlist);
for (j = 1; j < gt_dlist_size(dlist) / 2; j++)
dlistelem = gt_dlistelem_next(dlistelem);
gt_dlist_remove(dlist, dlistelem);
dlistelem = gt_dlist_first(dlist);
for (j = 1; j < gt_dlist_size(dlist) / 2 + 1; j++)
dlistelem = gt_dlistelem_next(dlistelem);
data = gt_dlistelem_get_data(gt_dlist_last(dlist));
ensure(had_err, *data == elems_backup[size / 2 + 1]);
}
#endif
gt_dlist_delete(dlist);
/* test without compare function */
dlist = gt_dlist_new(NULL);
ensure(had_err, !gt_dlist_size(dlist));
for (j = 0; j < size && !had_err; j++) {
gt_dlist_add(dlist, elems + j);
ensure(had_err, gt_dlist_size(dlist) == j+1);
}
j = 0;
for (dlistelem = gt_dlist_first(dlist); dlistelem != NULL;
dlistelem = gt_dlistelem_next(dlistelem)) {
data = gt_dlistelem_get_data(dlistelem);
ensure(had_err, *data == elems[j]);
j++;
}
/* remove first element */
if (gt_dlist_size(dlist)) {
gt_dlist_remove(dlist, gt_dlist_first(dlist));
if (gt_dlist_size(dlist)) {
data = gt_dlistelem_get_data(gt_dlist_first(dlist));
ensure(had_err, *data == elems[1]);
}
}
/* remove last element */
if (gt_dlist_size(dlist)) {
gt_dlist_remove(dlist, gt_dlist_last(dlist));
if (gt_dlist_size(dlist)) {
data = gt_dlistelem_get_data(gt_dlist_last(dlist));
ensure(had_err, *data == elems[size - 2]);
}
}
gt_dlist_delete(dlist);
}
return had_err;
}
