void gt_diagram_add_custom_track(GtDiagram *diagram, GtCustomTrack* ctrack)
{
gt_assert(diagram && ctrack);
gt_rwlock_wrlock(diagram->lock);
gt_array_add(diagram->custom_tracks, ctrack);
gt_rwlock_unlock(diagram->lock);
}
void gt_feature_index_delete(GtFeatureIndex *fi)
{
if (!fi) return;
gt_rwlock_wrlock(fi->pvt->lock);
if (fi->pvt->reference_count) {
fi->pvt->reference_count--;
gt_rwlock_unlock(fi->pvt->lock);
return;
}
gt_assert(fi->c_class);
if (fi->c_class->free)
fi->c_class->free(fi);
gt_rwlock_unlock(fi->pvt->lock);
gt_rwlock_delete(fi->pvt->lock);
gt_free(fi->pvt);
gt_free(fi);
}
GtFeatureIndex* gt_feature_index_ref(GtFeatureIndex *fi)
{
gt_assert(fi);
gt_rwlock_wrlock(fi->pvt->lock);
fi->pvt->reference_count++;
gt_rwlock_unlock(fi->pvt->lock);
return fi;
}
GtRange gt_diagram_get_range(const GtDiagram *diagram)
{
GtRange rng;
gt_assert(diagram);
gt_rwlock_rdlock(diagram->lock);
rng = diagram->range;
gt_rwlock_unlock(diagram->lock);
return rng;
}
GtArray* gt_diagram_get_custom_tracks(const GtDiagram *diagram)
{
GtArray *ret;
gt_assert(diagram);
gt_rwlock_rdlock(diagram->lock);
ret = diagram->custom_tracks;
gt_rwlock_unlock(diagram->lock);
return ret;
}
void gt_diagram_reset_track_selector_func(GtDiagram *diagram)
{
gt_assert(diagram);
gt_rwlock_wrlock(diagram->lock);
diagram->select_func = default_track_selector;
gt_hashmap_delete(diagram->blocks);
diagram->blocks = NULL;
gt_rwlock_unlock(diagram->lock);
}
GtStrArray* gt_feature_index_get_seqids(const GtFeatureIndex *feature_index,
GtError *err)
{
GtStrArray *strarr;
gt_assert(feature_index && feature_index->c_class);
gt_rwlock_rdlock(feature_index->pvt->lock);
strarr = feature_index->c_class->get_seqids(feature_index, err);
gt_rwlock_unlock(feature_index->pvt->lock);
return strarr;
}
int gt_feature_index_save(GtFeatureIndex *feature_index, GtError *err)
{
int ret;
gt_assert(feature_index && feature_index->c_class);
gt_assert(feature_index->c_class->save_func);
gt_rwlock_wrlock(feature_index->pvt->lock);
ret = feature_index->c_class->save_func(feature_index, err);
gt_rwlock_unlock(feature_index->pvt->lock);
return ret;
}
int gt_feature_index_remove_node(GtFeatureIndex *feature_index,
GtFeatureNode *node, GtError *err)
{
int ret;
gt_assert(feature_index && feature_index->c_class && node);
gt_rwlock_wrlock(feature_index->pvt->lock);
ret = feature_index->c_class->remove_node(feature_index, node, err);
gt_rwlock_unlock(feature_index->pvt->lock);
return ret;
}
char* gt_feature_index_get_first_seqid(const GtFeatureIndex
*feature_index,
GtError *err)
{
const char *str;
gt_assert(feature_index && feature_index->c_class);
gt_rwlock_rdlock(feature_index->pvt->lock);
str = feature_index->c_class->get_first_seqid(feature_index, err);
gt_rwlock_unlock(feature_index->pvt->lock);
return (char*) str;
}
GtArray* gt_feature_index_get_features_for_seqid(GtFeatureIndex *fi,
const char *seqid,
GtError *err)
{
GtArray *arr;
gt_assert(fi && fi->c_class && seqid);
gt_rwlock_rdlock(fi->pvt->lock);
arr = fi->c_class->get_features_for_seqid(fi, seqid, err);
gt_rwlock_unlock(fi->pvt->lock);
return arr;
}
int gt_feature_index_add_region_node(GtFeatureIndex *feature_index,
GtRegionNode *region_node,
GtError *err)
{
int ret;
gt_assert(feature_index && feature_index->c_class && region_node);
gt_rwlock_wrlock(feature_index->pvt->lock);
ret = feature_index->c_class->add_region_node(feature_index, region_node,
err);
gt_rwlock_unlock(feature_index->pvt->lock);
return ret;
}
int gt_feature_index_has_seqid(const GtFeatureIndex *feature_index,
bool *has_seqid,
const char *seqid,
GtError *err)
{
int ret;
gt_assert(feature_index && feature_index->c_class && seqid);
gt_rwlock_rdlock(feature_index->pvt->lock);
ret = feature_index->c_class->has_seqid(feature_index, has_seqid,
seqid, err);
gt_rwlock_unlock(feature_index->pvt->lock);
return ret;
}
int gt_feature_index_get_orig_range_for_seqid(GtFeatureIndex *feature_index,
GtRange *range,
const char *seqid,
GtError *err)
{
int ret;
gt_assert(feature_index && feature_index->c_class && range && seqid);
gt_rwlock_rdlock(feature_index->pvt->lock);
ret = feature_index->c_class->get_orig_range_for_seqid(feature_index, range,
seqid, err);
gt_rwlock_unlock(feature_index->pvt->lock);
return ret;
}
GtHashmap* gt_diagram_get_blocks(GtDiagram *diagram, GtError *err)
{
GtHashmap *ret;
int had_err = 0;
gt_assert(diagram);
gt_rwlock_wrlock(diagram->lock);
had_err = gt_diagram_build((GtDiagram*) diagram, err);
if (had_err)
ret = NULL;
else
ret = diagram->blocks;
gt_rwlock_unlock(diagram->lock);
return ret;
}
void gt_diagram_set_track_selector_func(GtDiagram *diagram,
GtTrackSelectorFunc bsfunc,
void *ptr)
{
gt_assert(diagram);
gt_rwlock_wrlock(diagram->lock);
/* register selector function and attached pointer */
diagram->select_func = bsfunc;
diagram->ptr = ptr;
/* this could change track assignment -> discard current blocks and requeue */
gt_hashmap_delete(diagram->blocks);
diagram->blocks = NULL;
gt_rwlock_unlock(diagram->lock);
}
void gt_layout_delete(GtLayout *layout)
{
if (!layout) return;
gt_rwlock_wrlock(layout->lock);
if (layout->twc && layout->own_twc)
gt_text_width_calculator_delete(layout->twc);
gt_hashmap_delete(layout->tracks);
gt_array_delete(layout->custom_tracks);
if (layout->blocks)
gt_hashmap_delete(layout->blocks);
gt_rwlock_unlock(layout->lock);
gt_rwlock_delete(layout->lock);
gt_free(layout);
}
int gt_feature_index_get_features_for_range(GtFeatureIndex *feature_index,
GtArray *results,
const char *seqid,
const GtRange *range, GtError *err)
{
int ret;
gt_assert(feature_index && feature_index->c_class && results && seqid &&
range);
gt_assert(gt_range_length(range) > 0);
gt_rwlock_rdlock(feature_index->pvt->lock);
ret = feature_index->c_class->get_features_for_range(feature_index, results,
seqid, range, err);
gt_rwlock_unlock(feature_index->pvt->lock);
return ret;
}
void gt_diagram_delete(GtDiagram *diagram)
{
if (!diagram) return;
gt_rwlock_wrlock(diagram->lock);
gt_array_delete(diagram->features);
if (diagram->blocks)
gt_hashmap_delete(diagram->blocks);
gt_hashmap_delete(diagram->nodeinfo);
gt_hashmap_delete(diagram->collapsingtypes);
gt_hashmap_delete(diagram->groupedtypes);
gt_hashmap_delete(diagram->caption_display_status);
gt_array_delete(diagram->custom_tracks);
gt_rwlock_unlock(diagram->lock);
gt_rwlock_delete(diagram->lock);
gt_free(diagram);
}
