static int add_to_parent(GtDiagram *d, GtFeatureNode *node, GtFeatureNode *parent, GtError *err) { GtBlock *block = NULL; NodeInfoElement *par_ni, *ni; gt_assert(d && node); if (!parent) return 0; par_ni = nodeinfo_get(d, parent); ni = nodeinfo_get(d, node); gt_log_log("adding %s to parent %p", gt_feature_node_get_type(node), parent); ni->parent = parent; block = nodeinfo_find_block(par_ni, gt_feature_node_get_type(node), parent); if (!block) { block = gt_block_new_from_node(parent); gt_block_set_type(block, gt_feature_node_get_type(node)); if (assign_block_caption(d, node, parent, block, err) < 0) { gt_block_delete(block); return -1; } nodeinfo_add_block(par_ni, gt_feature_node_get_type((GtFeatureNode*) node), parent, block); } gt_assert(block); gt_block_insert_element(block, node); return 0; }
static void blocklist_delete(void *value) { GtUword i; GtArray *a; if (!value) return; a = (GtArray*) value; for (i = 0; i < gt_array_size(a); i++) gt_block_delete(*(GtBlock**) gt_array_get(a, i)); gt_array_delete(a); }
static int add_to_current(GtDiagram *d, GtFeatureNode *node, GtFeatureNode *parent, GtError *err) { GtBlock *block; NodeInfoElement *ni; GtStyleQueryStatus rval; GtStr *caption = NULL; bool status = true; const char *nnid_p = NULL, *nnid_n = NULL, *nodetype; gt_assert(d && node); nodetype = gt_feature_node_get_type(node); if (get_caption_display_status(d, nodetype, &status, err) < 0) { return -1; } /* Get nodeinfo element and set itself as parent */ ni = nodeinfo_get(d, node); gt_log_log("adding %s to self", nodetype); ni->parent = node; /* create new GtBlock tuple and add to node info */ block = gt_block_new_from_node(node); caption = gt_str_new(); rval = gt_style_get_str(d->style, nodetype, "block_caption", caption, node, err); if (rval == GT_STYLE_QUERY_ERROR) { gt_str_delete(caption); gt_block_delete(block); return -1; } else if (rval == GT_STYLE_QUERY_NOT_SET) { nnid_p = get_node_name_or_id(parent); nnid_n = get_node_name_or_id(node); if ((nnid_p || nnid_n) && status) { if (parent) { if (nnid_p && gt_feature_node_has_children(parent)) gt_str_append_cstr(caption, nnid_p); else gt_str_append_cstr(caption, "-"); gt_str_append_cstr(caption, "/"); } if (nnid_n) gt_str_append_cstr(caption, nnid_n); } else { gt_str_delete(caption); caption = NULL; } } gt_block_set_caption(block, caption); gt_block_insert_element(block, node); nodeinfo_add_block(ni, gt_feature_node_get_type(node), GT_UNDEF_REPR, block); return 0; }
static int add_to_rep(GtDiagram *d, GtFeatureNode *node, GtFeatureNode* parent, GtError *err) { GtBlock *block = NULL; GtFeatureNode *rep = GT_UNDEF_REPR; NodeInfoElement *ni; gt_assert(d && node && gt_feature_node_is_multi(node)); rep = gt_feature_node_get_multi_representative(node); gt_log_log("adding %s to representative %p", gt_feature_node_get_type(node), rep); ni = nodeinfo_get(d, rep); block = nodeinfo_find_block(ni, gt_feature_node_get_type(node), rep); if (!block) { block = gt_block_new_from_node(parent); gt_block_set_type(block, gt_feature_node_get_type(node)); /* if parent is a pseudonode, then we have a multiline feature without a parent. we must not access the parent in this case! */ if (gt_feature_node_is_pseudo(parent)) { if (assign_block_caption(d, node, NULL, block, err) < 0) { gt_block_delete(block); return -1; } } else { if (assign_block_caption(d, node, parent, block, err) < 0) { gt_block_delete(block); return -1; } } nodeinfo_add_block(ni, gt_feature_node_get_type(node), rep, block); } gt_assert(block); gt_block_insert_element(block, node); return 0; }
int gt_block_unit_test(GtError *err) { GtRange r1, r2, r_temp, b_range; GtStrand s; GtGenomeNode *gn1, *gn2; GtElement *e1, *e2; double height; GtBlock *b; GtStr *seqid, *caption1, *caption2; int had_err = 0; GtStyle *sty; GtError *testerr; gt_error_check(err); seqid = gt_str_new_cstr("seqid"); caption1 = gt_str_new_cstr("foo"); caption2 = gt_str_new_cstr("bar"); testerr = gt_error_new(); r1.start = 10UL; r1.end = 50UL; r2.start = 40UL; r2.end = 50UL; gn1 = gt_feature_node_new(seqid, gt_ft_gene, r1.start, r1.end, GT_STRAND_FORWARD); gn2 = gt_feature_node_new(seqid, gt_ft_exon, r2.start, r2.end, GT_STRAND_FORWARD); e1 = gt_element_new((GtFeatureNode*) gn1); e2 = gt_element_new((GtFeatureNode*) gn2); b = gt_block_new(); /* test gt_block_insert_elements */ gt_ensure((0UL == gt_block_get_size(b))); gt_block_insert_element(b, (GtFeatureNode*) gn1); gt_ensure((1UL == gt_block_get_size(b))); gt_block_insert_element(b, (GtFeatureNode*) gn2); gt_ensure((2UL == gt_block_get_size(b))); /* test gt_block_set_range & gt_block_get_range */ r_temp = gt_range_join(&r1, &r2); gt_block_set_range(b, r_temp); b_range = gt_block_get_range(b); gt_ensure((0 == gt_range_compare(&b_range, &r_temp))); gt_ensure((1 == gt_range_compare(&r2, &r_temp))); /* tests gt_block_set_caption & gt_block_get_caption */ gt_block_set_caption(b, caption1); gt_ensure((0 == gt_str_cmp(gt_block_get_caption(b), caption1))); gt_ensure((0 != gt_str_cmp(gt_block_get_caption(b), caption2))); /* tests gt_block_set_strand & gt_block_get_range */ s = gt_block_get_strand(b); gt_ensure((GT_STRAND_UNKNOWN == s)); gt_block_set_strand(b, GT_STRAND_FORWARD); s = gt_block_get_strand(b); gt_ensure((GT_STRAND_FORWARD == s)); /* test gt_block_get_max_height() */ sty = gt_style_new(err); gt_ensure(gt_block_get_max_height(b, &height, sty, err) == 0); gt_ensure(!gt_error_is_set(testerr)); gt_ensure(height == BAR_HEIGHT_DEFAULT); gt_style_set_num(sty, "exon", "bar_height", 42); gt_ensure(gt_block_get_max_height(b, &height, sty, err) == 0); gt_ensure(!gt_error_is_set(testerr)); gt_ensure(height == 42); gt_style_set_num(sty, "gene", "bar_height", 23); gt_ensure(gt_block_get_max_height(b, &height, sty, err) == 0); gt_ensure(!gt_error_is_set(testerr)); gt_ensure(height == 42); gt_style_unset(sty, "exon", "bar_height"); gt_ensure(gt_block_get_max_height(b, &height, sty, err) == 0); gt_ensure(!gt_error_is_set(testerr)); gt_ensure(height == 23); gt_str_delete(caption2); gt_str_delete(seqid); gt_element_delete(e1); gt_element_delete(e2); gt_block_delete(b); gt_style_delete(sty); gt_error_delete(testerr); gt_genome_node_delete(gn1); gt_genome_node_delete(gn2); return had_err; }
int gt_track_unit_test(GtError *err) { int had_err = 0; GtBlock *b[4]; GtRange r[4]; GtTrack *track; GtGenomeNode *parent[4], *gn[4]; GtStr *title; double height, tmp; GtStyle *sty; unsigned long i; GtLineBreaker *lb; double t_rest = 0, l_rest = 0; gt_error_check(err); title = gt_str_new_cstr("test"); r[0].start=100UL; r[0].end=1000UL; r[1].start=1001UL; r[1].end=1500UL; r[2].start=700UL; r[2].end=1200UL; r[3].start=10UL; r[3].end=200UL; for (i=0; i<4; i++) { parent[i] = gt_feature_node_new(title, gt_ft_gene, r[i].start, r[i].end, GT_STRAND_FORWARD); gn[i] = gt_feature_node_new(title, gt_ft_exon, r[i].start, r[i].end, GT_STRAND_FORWARD); gt_feature_node_add_child((GtFeatureNode*) parent[i], (GtFeatureNode*) gn[i]); gt_feature_node_add_attribute((GtFeatureNode*) parent[i], GT_GFF_NAME, "parent"); gt_feature_node_add_attribute((GtFeatureNode*) gn[i], GT_GFF_NAME, "child"); } for (i=0; i<4; i++) { b[i] = gt_block_new(); gt_block_set_range(b[i], r[i]); gt_block_insert_element(b[i], (GtFeatureNode*) parent[i]); gt_block_insert_element(b[i], (GtFeatureNode*) gn[i]); } lb = gt_line_breaker_bases_new(); sty = gt_style_new(err); if (gt_style_get_num(sty, "format", "track_caption_font_size", &tmp, NULL, err) == GT_STYLE_QUERY_NOT_SET) { tmp = TEXT_SIZE_DEFAULT; } t_rest += tmp; if (gt_style_get_num(sty, "format", "track_caption_space", &tmp, NULL, err) == GT_STYLE_QUERY_NOT_SET) { tmp = CAPTION_BAR_SPACE_DEFAULT; } t_rest += tmp; if (gt_style_get_num(sty, "format", "track_vspace", &tmp, NULL, err) == GT_STYLE_QUERY_NOT_SET) { tmp = TRACK_VSPACE_DEFAULT; } t_rest += tmp; if (gt_style_get_num(sty, "format", "bar_vspace", &l_rest, NULL, err) == GT_STYLE_QUERY_NOT_SET) { l_rest = BAR_VSPACE_DEFAULT; } track = gt_track_new(title, GT_UNDEF_ULONG, true, lb); gt_ensure(had_err, track); gt_ensure(had_err, gt_track_get_title(track) == title); gt_ensure(had_err, gt_track_get_number_of_lines(track) == 0); gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0); gt_ensure(had_err, height == t_rest); gt_ensure(had_err, !gt_error_is_set(err)); gt_ensure(had_err, gt_track_insert_block(track, b[0], err) == 0); gt_ensure(had_err, !gt_error_is_set(err)); gt_ensure(had_err, gt_track_get_number_of_lines(track) == 1); gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0); gt_ensure(had_err, height == t_rest + l_rest + BAR_HEIGHT_DEFAULT); gt_ensure(had_err, !gt_error_is_set(err)); gt_ensure(had_err, gt_track_insert_block(track, b[1], err) == 0); gt_ensure(had_err, !gt_error_is_set(err)); gt_ensure(had_err, gt_track_get_number_of_lines(track) == 1); gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0); gt_ensure(had_err, height == t_rest + l_rest + BAR_HEIGHT_DEFAULT); gt_ensure(had_err, !gt_error_is_set(err)); gt_ensure(had_err, gt_track_insert_block(track, b[2], err) == 0); gt_ensure(had_err, !gt_error_is_set(err)); gt_ensure(had_err, gt_track_get_number_of_lines(track) == 2); gt_ensure(had_err, gt_track_insert_block(track, b[3], err) == 0); gt_ensure(had_err, !gt_error_is_set(err)); gt_ensure(had_err, gt_track_get_number_of_lines(track) == 2); gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0); gt_ensure(had_err, height == t_rest + 2*(l_rest + BAR_HEIGHT_DEFAULT)); gt_ensure(had_err, !gt_error_is_set(err)); gt_style_set_num(sty, "exon", "bar_height", 42); gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0); gt_ensure(had_err, height == t_rest + 2*(l_rest+42)); gt_ensure(had_err, !gt_error_is_set(err)); gt_style_set_num(sty, "gene", "bar_height", 23); gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0); gt_ensure(had_err, height == t_rest + 2*(l_rest+42)); gt_ensure(had_err, !gt_error_is_set(err)); gt_style_unset(sty, "exon", "bar_height"); gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0); gt_ensure(had_err, height == t_rest + 2*(l_rest+23)); gt_ensure(had_err, !gt_error_is_set(err)); gt_style_unset(sty, "gene", "bar_height"); gt_style_set_num(sty, "format", "bar_height", 99); gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0); gt_ensure(had_err, height == t_rest + 2*(l_rest+99)); gt_ensure(had_err, !gt_error_is_set(err)); gt_ensure(had_err, gt_track_get_number_of_discarded_blocks(track) == 0); gt_track_delete(track); gt_str_delete(title); gt_style_delete(sty); for (i=0; i<4; i++) { gt_block_delete(b[i]); gt_genome_node_delete(parent[i]); } return had_err; }
/* Create lists of all GtBlocks in the diagram. */ static int collect_blocks(GT_UNUSED void *key, void *value, void *data, GT_UNUSED GtError *err) { NodeInfoElement *ni = (NodeInfoElement*) value; GtDiagram *diagram = (GtDiagram*) data; GtBlock *block = NULL; GtStr *trackid_str; GtUword i = 0; trackid_str = gt_str_new(); for (i = 0; i < gt_str_array_size(ni->types); i++) { const char *type; GtUword j; GtArray *list; PerTypeInfo *type_struc = NULL; GtBlock* mainblock = NULL; type = gt_str_array_get(ni->types, i); type_struc = gt_hashmap_get(ni->type_index, type); gt_assert(type_struc); for (j=0; j<gt_array_size(type_struc->blocktuples); j++) { GtBlockTuple *bt; bt = *(GtBlockTuple**) gt_array_get(type_struc->blocktuples, j); if (bt->rep == GT_UNDEF_REPR && type_struc->must_merge) { block = mainblock = gt_block_ref(bt->block); gt_block_delete(mainblock); gt_free(bt); continue; } else { if (mainblock) { block = gt_block_clone(mainblock); gt_block_merge(block, bt->block); gt_block_delete(bt->block); } else block = bt->block; } gt_assert(block); gt_str_reset(trackid_str); /* execute hook for track selector function */ diagram->select_func(block, trackid_str, diagram->ptr); if (!(list = (GtArray*) gt_hashmap_get(diagram->blocks, gt_str_get(trackid_str)))) { list = gt_array_new(sizeof (GtBlock*)); gt_hashmap_add(diagram->blocks, gt_cstr_dup(gt_str_get(trackid_str)), list); }; gt_assert(list); gt_array_add(list, block); gt_free(bt); } gt_array_delete(type_struc->blocktuples); gt_hashmap_delete(type_struc->rep_index); gt_block_delete(mainblock); } gt_hashmap_delete(ni->type_index); gt_str_array_delete(ni->types); gt_free(ni); gt_str_delete(trackid_str); return 0; }