bool gt_type_graph_is_partof(GtTypeGraph *type_graph, const char *parent_type,
const char *child_type)
{
const char *parent_id, *child_id;
GtTypeNode *parent_node, *child_node;
gt_assert(type_graph && parent_type && child_type);
/* make sure graph is built */
if (!type_graph->ready) {
create_vertices(type_graph);
type_graph->ready = true;
}
/* get parent ID, if the type is not mappable to an ID, assume it is the ID */
if (!(parent_id = gt_hashmap_get(type_graph->name2id, parent_type)))
parent_id = parent_type;
/* get child ID, if the type is not mappable to an ID, assmue it is the ID */
if (!(child_id = gt_hashmap_get(type_graph->name2id, child_type)))
child_id = child_type;
/* get parent node */
parent_node = gt_hashmap_get(type_graph->nodemap, parent_id);
gt_assert(parent_node);
/* get child node */
child_node = gt_hashmap_get(type_graph->nodemap, child_id);
gt_assert(child_node);
/* check for parent */
return gt_type_node_has_parent(child_node, parent_node,
type_graph->part_of_out_edges,
type_graph->part_of_in_edges,
type_graph->nodes, type_graph->id2name, 0);
}
static GtFeatureNode* find_root(const GtFeatureInfo *fi, const char *id)
{
const char *delim, *parents;
GtFeatureNode *this_feature, *parent_pseudo_feature;
gt_assert(fi && id);
/* get feature */
delim = strchr(id, ';');
if (delim) {
char *first_parent = gt_cstr_dup_nt(id, delim - id);
this_feature = gt_hashmap_get(fi->id_to_genome_node, first_parent);
parent_pseudo_feature = gt_hashmap_get(fi->id_to_pseudo_parent,
first_parent);
gt_free(first_parent);
}
else {
this_feature = gt_hashmap_get(fi->id_to_genome_node, id);
parent_pseudo_feature = gt_hashmap_get(fi->id_to_pseudo_parent, id);
}
gt_assert(this_feature);
/* recursion */
parents = gt_feature_node_get_attribute(this_feature, GT_GFF_PARENT);
if (parents)
return find_root(fi, parents);
else if (parent_pseudo_feature)
return parent_pseudo_feature;
return this_feature;
}
void gt_free_mem(void *ptr, GT_UNUSED const char *src_file,
GT_UNUSED int src_line)
{
MAInfo *mainfo;
gt_assert(ma);
if (ptr == NULL) return;
if (ma->bookkeeping) {
gt_mutex_lock(bookkeeping_lock);
#ifndef NDEBUG
if (!gt_hashmap_get(ma->allocated_pointer, ptr)) {
fprintf(stderr, "bug: double free() attempted on line %d in file "
"\"%s\"\n", src_line, src_file);
exit(GT_EXIT_PROGRAMMING_ERROR);
}
#endif
mainfo = gt_hashmap_get(ma->allocated_pointer, ptr);
gt_assert(mainfo);
subtract_size(ma, mainfo->size);
gt_hashmap_remove(ma->allocated_pointer, ptr);
free(ptr);
gt_mutex_unlock(bookkeeping_lock);
}
else {
free(ptr);
}
}
static void create_vertices(GtTypeGraph *type_graph)
{
GtUword i, j;
GtTypeNode *parent;
const char *id;
gt_assert(type_graph && !type_graph->ready);
/* iterate over nodes */
for (i = 0; i < gt_array_size(type_graph->nodes); i++) {
GtTypeNode *node = *(GtTypeNode**) gt_array_get(type_graph->nodes, i);
/* process is_a parents */
for (j = 0; j < gt_type_node_is_a_size(node); j++) {
id = gt_type_node_is_a_get(node, j);
parent = gt_hashmap_get(type_graph->nodemap, id);
gt_assert(parent);
gt_type_node_add_is_a_vertex(node, parent);
}
/* process part_of parents */
for (j = 0; j < gt_type_node_part_of_size(node); j++) {
id = gt_type_node_part_of_get(node, j);
parent = gt_hashmap_get(type_graph->nodemap, id);
gt_assert(parent);
gt_bool_matrix_set(type_graph->part_of_out_edges, gt_type_node_num(node),
gt_type_node_num(parent), true);
gt_bool_matrix_set(type_graph->part_of_in_edges, gt_type_node_num(parent),
gt_type_node_num(node), true);
}
}
}
static int gt_orf_finder_visitor_feature_node(GtNodeVisitor *gv,
GtFeatureNode *gf,
GtError *err)
{
GtORFFinderVisitor *lv;
const char *gft = NULL;
GtFeatureNodeIterator *gfi;
GtFeatureNode *curnode = NULL;
int had_err = 0;
GtRange rng;
lv = gt_orf_finder_visitor_cast(gv);
gt_assert(lv);
gt_error_check(err);
gfi = gt_feature_node_iterator_new(gf);
while (!had_err && (curnode = gt_feature_node_iterator_next(gfi))) {
gft = gt_feature_node_get_type(curnode);
if (gt_hashmap_get(lv->types, (void*) gft) != NULL ||
gt_hashmap_get(lv->types,
(void*) "all") == (void*) 1) {
if (!had_err) {
rng = gt_genome_node_get_range((GtGenomeNode*) curnode);
had_err = run_orffinder(lv->rmap, curnode, rng.start - 1, rng.end - 1,
lv->min, lv->max, lv->all, err);
if (gt_hashmap_get(lv->types,
(void*) "all") == (void*) 1) {
break;
}
else if (gt_feature_node_has_children(curnode)) {
GtFeatureNode *tmpnode = NULL;
GtFeatureNodeIterator *tmpgfi = gt_feature_node_iterator_new(curnode);
(void) gt_feature_node_iterator_next(tmpgfi);
while ((tmpnode = gt_feature_node_iterator_next(tmpgfi))) {
gft = gt_feature_node_get_type(tmpnode);
if (strcmp(gft, (const char*) GT_ORF_TYPE) == 0) {
continue;
}
/* curnode = gt_feature_node_iterator_next(gfi); */
}
gt_feature_node_iterator_delete(tmpgfi);
}
}
}
}
gt_feature_node_iterator_delete(gfi);
return had_err;
}
static GtBlock* nodeinfo_find_block(NodeInfoElement* ni, const char *gft,
GtFeatureNode *fn)
{
PerTypeInfo *type_struc = NULL;
GtBlockTuple *bt = NULL;
gt_assert(ni);
if (!(type_struc = gt_hashmap_get(ni->type_index, gft)))
return NULL;
if (!(bt = gt_hashmap_get(type_struc->rep_index, fn)))
return NULL;
gt_assert(bt);
return bt->block;
}
static int gff3_show_feature_node(GtFeatureNode *fn, void *data,
GT_UNUSED GtError *err)
{
bool part_shown = false;
GtGFF3Visitor *gff3_visitor = (GtGFF3Visitor*) data;
GtArray *parent_features = NULL;
ShowAttributeInfo info;
GtUword i;
GtStr *id;
gt_error_check(err);
gt_assert(fn && gff3_visitor);
/* output leading part */
gt_gff3_output_leading(fn, gff3_visitor->outfp);
/* show unique id part of attributes */
if ((id = gt_hashmap_get(gff3_visitor->feature_node_to_unique_id_str, fn))) {
gt_file_xprintf(gff3_visitor->outfp, "%s=%s", GT_GFF_ID, gt_str_get(id));
part_shown = true;
}
/* show parent part of attributes */
parent_features = gt_hashmap_get(gff3_visitor->feature_node_to_id_array, fn);
if (gt_array_size(parent_features)) {
if (part_shown)
gt_file_xfputc(';', gff3_visitor->outfp);
gt_file_xprintf(gff3_visitor->outfp, "%s=", GT_GFF_PARENT);
for (i = 0; i < gt_array_size(parent_features); i++) {
if (i)
gt_file_xfputc(',', gff3_visitor->outfp);
gt_file_xprintf(gff3_visitor->outfp, "%s",
*(char**) gt_array_get(parent_features, i));
}
part_shown = true;
}
/* show missing part of attributes */
info.attribute_shown = &part_shown;
info.outfp = gff3_visitor->outfp;
gt_feature_node_foreach_attribute(fn, show_attribute, &info);
/* show dot if no attributes have been shown */
if (!part_shown)
gt_file_xfputc('.', gff3_visitor->outfp);
/* show terminal newline */
gt_file_xfputc('\n', gff3_visitor->outfp);
return 0;
}
int main(int argc, char **argv)
{
if(argc != 2)
{
fputs("usage: vang schema.file\n", stderr);
return 1;
}
gt_lib_init();
char *schemafile = argv[1];
FILE *schema = fopen(schemafile, "r");
if(schema == NULL)
{
fprintf(stderr, "error: unable to open schema file '%s'\n", schemafile);
return 1;
}
GtArray *entry_datatypes = gt_array_new( sizeof(char *) );
GtHashmap *entries = gt_hashmap_new( GT_HASH_STRING, NULL,
(GtFree)vang_schema_entry_delete );
VangSchemaEntry *entry;
while( (entry = vang_schema_entry_next(schema)) != NULL )
{
char *datatype = (char *)vang_schema_entry_get_datatype(entry);
VangSchemaEntry *testentry = gt_hashmap_get(entries, datatype);
if(testentry != NULL)
{
fprintf( stderr, "warning: already have an entry for data type '%s'; "
"replacing\n", datatype );
vang_schema_entry_delete(testentry);
}
gt_hashmap_add(entries, datatype, entry);
gt_array_add(entry_datatypes, datatype);
}
unsigned long i;
for(i = 0; i < gt_array_size(entry_datatypes); i++)
{
const char *type = *(const char **)gt_array_get(entry_datatypes, i);
VangSchemaEntry *entry = gt_hashmap_get(entries, type);
vang_schema_entry_to_string(entry, stdout);
puts("");
}
gt_array_delete(entry_datatypes);
gt_hashmap_delete(entries);
gt_lib_clean();
return 0;
}
static GtHpolProcessorAddToHashResult gt_hpol_processor_add_segment_to_hashmap(
GtHpolProcessor *hpp, GtAlignedSegment *as)
{
GtAlignedSegment *stored_as;
if ((stored_as = gt_hashmap_get(hpp->processed_segments,
gt_aligned_segment_description(as))) != NULL)
{
hpp->nof_multihits++;
if (!gt_aligned_segment_seq_edited(stored_as) &&
gt_aligned_segment_seq_edited(as))
{
hpp->nof_replaced++;
/* change with newly edited as */
gt_hashmap_remove(hpp->processed_segments,
(void*)gt_aligned_segment_description(as));
gt_hashmap_add(hpp->processed_segments,
(void*)gt_aligned_segment_description(as), as);
return GT_HPOL_PROCESSOR_REPLACED;
}
/* otherwise discard (todo: implement combination of edits) */
else
{
return GT_HPOL_PROCESSOR_NOT_REPLACED;
}
}
else
{
gt_hashmap_add(hpp->processed_segments,
(void*)gt_aligned_segment_description(as), as);
return GT_HPOL_PROCESSOR_NEW_RECORD;
}
}
void* gt_realloc_mem(void *ptr, size_t size, const char *src_file, int src_line)
{
MAInfo *mainfo;
void *mem;
gt_assert(ma);
if (ma->bookkeeping) {
gt_mutex_lock(bookkeeping_lock);
ma->mallocevents++;
if (ptr) {
mainfo = gt_hashmap_get(ma->allocated_pointer, ptr);
gt_assert(mainfo);
subtract_size(ma, mainfo->size);
gt_hashmap_remove(ma->allocated_pointer, ptr);
}
mainfo = xmalloc(sizeof *mainfo, ma->current_size, src_file, src_line);
mainfo->size = size;
mainfo->src_file = src_file;
mainfo->src_line = src_line;
mem = xrealloc(ptr, size, ma->current_size, src_file, src_line);
gt_hashmap_add(ma->allocated_pointer, mem, mainfo);
add_size(ma, size);
gt_mutex_unlock(bookkeeping_lock);
return mem;
}
return xrealloc(ptr, size, ma->current_size, src_file, src_line);
}
bool gt_toolbox_has_tool(const GtToolbox *tb, const char *toolname)
{
gt_assert(tb && tb->tools);
if (gt_hashmap_get(tb->tools, toolname))
return true;
return false;
}
static int gt_regioncov_visitor_feature_node(GtNodeVisitor *nv,
GtFeatureNode *fn,
GT_UNUSED GtError *err)
{
GtRange *old_range_ptr, old_range, new_range;
GtArray *ranges;
GtRegionCovVisitor *regioncov_visitor;
gt_error_check(err);
regioncov_visitor = gt_regioncov_visitor_cast(nv);
ranges = gt_hashmap_get(regioncov_visitor->region2rangelist,
gt_str_get(gt_genome_node_get_seqid((GtGenomeNode*)
fn)));
gt_assert(ranges);
new_range = gt_genome_node_get_range((GtGenomeNode*) fn);
if (!gt_array_size(ranges))
gt_array_add(ranges, new_range);
else {
old_range_ptr = gt_array_get_last(ranges);
old_range = *old_range_ptr;
old_range.end += regioncov_visitor->max_feature_dist;
if (gt_range_overlap(&old_range, &new_range)) {
old_range_ptr->end = MAX(old_range_ptr->end, new_range.end);
}
else
gt_array_add(ranges, new_range);
}
return 0;
}
void gt_type_graph_add_stanza(GtTypeGraph *type_graph,
const GtOBOStanza *stanza)
{
const char *id_value, *name_value;
GtUword i, size;
GtTypeNode *node;
GtStr *buf;
gt_assert(type_graph && stanza && !type_graph->ready);
gt_assert(gt_obo_stanza_size(stanza, "id") == 1);
gt_assert(gt_obo_stanza_size(stanza, "name") == 1);
id_value = gt_symbol(gt_obo_stanza_get_value(stanza, "id", 0));
name_value = gt_symbol(gt_obo_stanza_get_value(stanza, "name", 0));
gt_assert(id_value);
gt_assert(name_value);
gt_assert(!gt_hashmap_get(type_graph->nodemap, id_value));
node = gt_type_node_new(gt_array_size(type_graph->nodes), id_value);
gt_hashmap_add(type_graph->name2id, (char*) name_value, (char*) id_value);
gt_hashmap_add(type_graph->id2name, (char*) id_value, (char*) name_value);
gt_hashmap_add(type_graph->nodemap, (char*) id_value, node);
gt_array_add(type_graph->nodes, node);
buf = gt_str_new();
/* store is_a entries in node, if necessary */
if ((size = gt_obo_stanza_size(stanza, "is_a"))) {
for (i = 0; i < size; i++) {
const char *id = gt_obo_stanza_get_value(stanza, "is_a", i);
gt_str_reset(buf);
gt_str_append_cstr_nt(buf, id, strcspn(id, " \n"));
gt_type_node_is_a_add(node, gt_symbol(gt_str_get(buf)));
}
}
/* store part_of entries in node, if necessary */
if ((size = gt_obo_stanza_size(stanza, "relationship"))) {
for (i = 0; i < size; i++) {
const char *rel = gt_obo_stanza_get_value(stanza, "relationship", i);
gt_str_reset(buf);
/* match part_of */
if (!strncmp(rel, PART_OF, strlen(PART_OF))) {
const char *part_of = rel + strlen(PART_OF) + 1;
gt_str_append_cstr_nt(buf, part_of, strcspn(part_of, " \n"));
gt_type_node_part_of_add(node, gt_symbol(gt_str_get(buf)));
continue;
}
/* match member_of */
if (!strncmp(rel, MEMBER_OF, strlen(MEMBER_OF))) {
const char *member_of = rel + strlen(MEMBER_OF) + 1;
gt_str_append_cstr_nt(buf, member_of, strcspn(member_of, " \n"));
gt_type_node_part_of_add(node, gt_symbol(gt_str_get(buf)));
continue;
}
/* match integral_part_of */
if (!strncmp(rel, INTEGRAL_PART_OF, strlen(INTEGRAL_PART_OF))) {
const char *integral_part_of = rel + strlen(INTEGRAL_PART_OF) + 1;
gt_str_append_cstr_nt(buf, integral_part_of,
strcspn(integral_part_of, " \n"));
gt_type_node_part_of_add(node, gt_symbol(gt_str_get(buf)));
}
}
}
gt_str_delete(buf);
}
GtTool* gt_toolbox_get_tool(GtToolbox *tb, const char *toolname)
{
GtToolinfo *toolinfo;
gt_assert(tb && tb->tools);
toolinfo = gt_hashmap_get(tb->tools, toolname);
if (toolinfo)
return toolinfo->tool;
return NULL;
}
const char* gt_xrf_abbr_entry_get_value(const GtXRFAbbrEntry *abbr_entry,
const char *entry_key)
{
GtStr *s;
gt_assert(abbr_entry);
if ((s = gt_hashmap_get(abbr_entry->content, entry_key)))
return gt_str_get(s);
return NULL;
}
void gt_xrf_abbr_entry_add(GtXRFAbbrEntry *abbr_entry, const char *tag,
const char *value)
{
GtStr *s;
gt_assert(abbr_entry && tag && value);
if (!(s = gt_hashmap_get(abbr_entry->content, tag))) {
s = gt_str_new_cstr(value);
gt_hashmap_add(abbr_entry->content, gt_cstr_dup(tag), s);
}
}
static void gt_hmmer_parse_status_mark_frame_finished(GtHMMERParseStatus *s)
{
GtHMMERModelHit *mh;
gt_assert(s && s->models);
mh = gt_hashmap_get(s->models, gt_str_get(s->cur_model));
if (mh != NULL) {
mh->last_array_size_fwd = gt_array_size(mh->fwd_hits);
mh->last_array_size_rev = gt_array_size(mh->rev_hits);
}
}
static int filter_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
GtError *error)
{
AgnFilterStream *stream;
GtFeatureNode *fn;
int had_err;
gt_error_check(error);
stream = filter_stream_cast(ns);
if(gt_queue_size(stream->cache) > 0)
{
*gn = gt_queue_get(stream->cache);
return 0;
}
while(1)
{
had_err = gt_node_stream_next(stream->in_stream, gn, error);
if(had_err)
return had_err;
if(!*gn)
return 0;
fn = gt_feature_node_try_cast(*gn);
if(!fn)
return 0;
GtFeatureNode *current;
GtFeatureNodeIterator *iter = gt_feature_node_iterator_new(fn);
for(current = gt_feature_node_iterator_next(iter);
current != NULL;
current = gt_feature_node_iterator_next(iter))
{
const char *type = gt_feature_node_get_type(current);
bool keepfeature = false;
if(gt_hashmap_get(stream->typestokeep, type) != NULL)
keepfeature = true;
if(keepfeature)
{
gt_genome_node_ref((GtGenomeNode *)current);
gt_queue_add(stream->cache, current);
}
}
gt_feature_node_iterator_delete(iter);
gt_genome_node_delete((GtGenomeNode *)fn);
if(gt_queue_size(stream->cache) > 0)
{
*gn = gt_queue_get(stream->cache);
return 0;
}
}
return 0;
}
static int handle_description(GtSeqid2SeqnumMapping *mapping, const char *desc,
GtUword seqnum, GtUword filenum,
GtError *err)
{
GtRange descrange;
GtUword j;
int had_err = 0;
SeqidInfo *seqid_info;
if (gt_parse_description_range(desc, &descrange)) {
/* no offset could be parsed -> store description as sequence id */
descrange.start = 1;
descrange.end = GT_UNDEF_UWORD;
if ((seqid_info = gt_hashmap_get(mapping->map, desc))) {
had_err = seqid_info_add(seqid_info, seqnum, filenum,
&descrange, mapping->filename, desc, err);
gt_assert(had_err); /* adding a seqid without range should fail */
}
else {
seqid_info = seqid_info_new(seqnum, filenum, &descrange);
gt_hashmap_add(mapping->map, gt_cstr_dup(desc), seqid_info);
}
} else {
char *dup;
/* offset could be parsed -> store description up to ':' as sequence id */
j = 0;
while (desc[j] != ':')
j++;
dup = gt_malloc((j + 1) * sizeof *dup);
strncpy(dup, desc, j);
dup[j] = '\0';
if ((seqid_info = gt_hashmap_get(mapping->map, dup))) {
had_err = seqid_info_add(seqid_info, seqnum, filenum, &descrange,
mapping->filename, dup, err);
gt_free(dup);
}
else {
seqid_info = seqid_info_new(seqnum, filenum, &descrange);
gt_hashmap_add(mapping->map, dup, seqid_info);
}
}
return had_err;
}
static GtStr* get_seqid(GtBEDParser *bed_parser)
{
GtStr *seqid = gt_hashmap_get(bed_parser->seqid_to_str_mapping,
gt_str_get(bed_parser->word));
if (!seqid) {
seqid = gt_str_new_cstr(gt_str_get(bed_parser->word));
gt_hashmap_add(bed_parser->seqid_to_str_mapping, gt_str_get(seqid), seqid);
}
gt_assert(seqid);
return seqid;
}
static NodeInfoElement* nodeinfo_get(GtDiagram *d, GtFeatureNode *node)
{
NodeInfoElement *ni;
gt_assert(d && node);
if (!(ni = gt_hashmap_get(d->nodeinfo, node))) {
ni = gt_calloc(1, sizeof (NodeInfoElement));
ni->type_index = gt_hashmap_new(GT_HASH_STRING, NULL, gt_free_func);
ni->types = gt_str_array_new();
gt_hashmap_add(d->nodeinfo, node, ni);
}
return ni;
}
GtUword gt_md5_tab_map(GtMD5Tab *md5_tab, const char *md5)
{
const char *value;
gt_assert(md5_tab && md5);
if (!md5_tab->md5map)
build_md5map(md5_tab);
gt_assert(md5_tab->md5map);
value = gt_hashmap_get(md5_tab->md5map, md5);
if (value)
return ((GtUword) value) - 1;
return GT_UNDEF_UWORD;
}
static int add_id(GtFeatureNode *fn, void *data, GT_UNUSED GtError *err)
{
AddIDInfo *info = (AddIDInfo*) data;
GtArray *parent_features = NULL;
gt_error_check(err);
gt_assert(fn && info && info->gt_feature_node_to_id_array && info->id);
parent_features = gt_hashmap_get(info->gt_feature_node_to_id_array, fn);
if (!parent_features) {
parent_features = gt_array_new(sizeof (char*));
gt_hashmap_add(info->gt_feature_node_to_id_array, fn, parent_features);
}
gt_array_add(parent_features, info->id);
return 0;
}
bool gt_line_breaker_bases_is_line_occupied(GtLineBreaker* lb, GtLine *line,
GtBlock *block)
{
GtLineBreakerBases *lbb;
GtRange r;
GtIntervalTree *t;
gt_assert(lb && block && line);
r = gt_block_get_range(block);
lbb = gt_line_breaker_bases_cast(lb);
if (!(t = gt_hashmap_get(lbb->itrees, line)))
return false;
else
return (gt_interval_tree_find_first_overlapping(t, r.start, r.end));
}
static int check_cds_phases_if_necessary(GtFeatureNode *fn,
GtCDSCheckVisitor *v,
bool second_pass, GtError *err)
{
GtFeatureNodeIterator *fni;
GtFeatureNode *node;
GtArray *cds_features = NULL;
GtHashmap *multi_features = NULL;
int had_err = 0;
gt_error_check(err);
gt_assert(fn);
fni = gt_feature_node_iterator_new_direct(fn);
while ((node = gt_feature_node_iterator_next(fni))) {
if (gt_feature_node_has_type(node, gt_ft_CDS)) {
if (gt_feature_node_is_multi(node)) {
GtArray *features;
if (!multi_features)
multi_features = gt_hashmap_new(GT_HASH_DIRECT, NULL,
(GtFree) gt_array_delete);
if ((features =
gt_hashmap_get(multi_features,
gt_feature_node_get_multi_representative(node)))) {
gt_array_add(features, node);
}
else {
GtFeatureNode *representative;
features = gt_array_new(sizeof (GtFeatureNode*));
representative = gt_feature_node_get_multi_representative(node);
gt_array_add(features, representative);
gt_hashmap_add(multi_features, representative, features);
}
}
else {
if (!cds_features)
cds_features = gt_array_new(sizeof (GtFeatureNode*));
gt_array_add(cds_features, node);
}
}
}
if (cds_features)
had_err = check_cds_phases(cds_features, v, false, second_pass, err);
if (!had_err && multi_features)
had_err = gt_hashmap_foreach(multi_features, check_cds_phases_hm, v, err);
gt_array_delete(cds_features);
gt_hashmap_delete(multi_features);
gt_feature_node_iterator_delete(fni);
return had_err;
}
static int run_tests(GtR *gtr, GtError *err)
{
int test_err = 0, had_err = 0;
char* key;
void* value;
gt_error_check(err);
gt_assert(gtr);
/* The following type assumptions are made in the GenomeTools library. */
gt_ensure(sizeof (char) == 1);
gt_ensure(sizeof (unsigned char) == 1);
gt_ensure(sizeof (short) == 2);
gt_ensure(sizeof (unsigned short) == 2);
gt_ensure(sizeof (int) == 4);
gt_ensure(sizeof (unsigned int) == 4);
gt_ensure(sizeof (GtWord) == 4 || sizeof (GtWord) == 8);
gt_ensure(sizeof (GtUword) == 4 || sizeof (GtUword) == 8);
gt_ensure(sizeof (GtUword) >= sizeof (size_t));
gt_ensure(sizeof (GtInt64) == 8);
gt_ensure(sizeof (GtUint64) == 8);
/* show seed */
printf("seed=%u\n", gtr->seed);
gt_hashmap_unit_test(err);
if (gtr->unit_tests) {
if (gt_str_length(gtr->test_only) > 0) {
key = gt_str_get(gtr->test_only);
value = gt_hashmap_get(gtr->unit_tests, key);
if (value) {
had_err = gt_unit_test_run(key, value, &test_err, err);
gt_assert(!had_err); /* cannot happen, gt_unit_test_run() is sane */
}
else {
gt_error_set(err, "Test \"%s\" not found", key);
return EXIT_FAILURE;
}
}
else {
had_err = gt_hashmap_foreach_in_key_order(gtr->unit_tests,
gt_unit_test_run, &test_err,
err);
gt_assert(!had_err); /* cannot happen, gt_unit_test_run() is sane */
}
}
if (test_err)
return EXIT_FAILURE;
return EXIT_SUCCESS;
}
int gt_line_breaker_bases_is_line_occupied(GtLineBreaker* lb, bool *result,
GtLine *line, GtBlock *block,
GT_UNUSED GtError *err)
{
GtLineBreakerBases *lbb;
GtRange r;
GtIntervalTree *t;
gt_assert(lb && block && line);
r = gt_block_get_range(block);
lbb = gt_line_breaker_bases_cast(lb);
if (!(t = gt_hashmap_get(lbb->itrees, line)))
*result = false;
else
*result = (gt_interval_tree_find_first_overlapping(t, r.start, r.end));
return 0; /* gt_line_breaker_bases_is_line_occupied() is sane */
}
static int store_ids(GtFeatureNode *fn, void *data, GtError *err)
{
GtGFF3Visitor *gff3_visitor = (GtGFF3Visitor*) data;
AddIDInfo add_id_info;
int had_err = 0;
GtStr *id;
gt_error_check(err);
gt_assert(fn && gff3_visitor);
if (gt_feature_node_has_children(fn) || gt_feature_node_is_multi(fn) ||
(gff3_visitor->retain_ids && gt_feature_node_get_attribute(fn, "ID"))) {
if (gt_feature_node_is_multi(fn)) {
id = gt_hashmap_get(gff3_visitor->feature_node_to_unique_id_str,
gt_feature_node_get_multi_representative(fn));
if (!id) {
/* the representative does not have its own id yet -> create it */
if (gff3_visitor->retain_ids) {
id = make_id_unique(gff3_visitor,
gt_feature_node_get_multi_representative(fn));
}
else {
id = create_unique_id(gff3_visitor,
gt_feature_node_get_multi_representative(fn));
}
}
/* store id for feature, if the feature was not the representative */
if (gt_feature_node_get_multi_representative(fn) != fn) {
gt_hashmap_add(gff3_visitor->feature_node_to_unique_id_str, fn,
gt_str_ref(id));
}
}
else {
if (gff3_visitor->retain_ids)
id = make_id_unique(gff3_visitor, fn);
else
id = create_unique_id(gff3_visitor, fn);
}
/* for each child -> store the parent feature in the hash map */
add_id_info.gt_feature_node_to_id_array =
gff3_visitor->feature_node_to_id_array,
add_id_info.id = gt_str_get(id);
had_err = gt_feature_node_traverse_direct_children(fn, &add_id_info, add_id,
err);
}
return had_err;
}
static int get_caption_display_status(GtDiagram *d, const char *gft,
bool *result, GtError *err)
{
bool *status;
gt_assert(d && gft);
status = (bool*) gt_hashmap_get(d->caption_display_status, gft);
if (!status)
{
GtUword threshold = GT_UNDEF_UWORD;
double tmp = GT_UNDEF_DOUBLE;
status = gt_malloc(sizeof (bool));
*status = true;
if (gt_style_get_bool(d->style, "format", "show_block_captions", status,
NULL, err) == GT_STYLE_QUERY_ERROR) {
gt_free(status);
return -1;
}
if (*status)
{
GtStyleQueryStatus rval;
rval = gt_style_get_num(d->style,
gft, "max_capt_show_width",
&tmp, NULL, err);
switch (rval) {
case GT_STYLE_QUERY_ERROR:
gt_free(status);
return -1;
break; /* should never reach this */
case GT_STYLE_QUERY_NOT_SET:
*status = true;
break;
default:
gt_assert(tmp != GT_UNDEF_DOUBLE);
threshold = tmp;
gt_assert(tmp != GT_UNDEF_UWORD);
*status = (gt_range_length(&d->range) <= threshold);
break;
}
*status = (gt_range_length(&d->range) <= threshold);
}
gt_hashmap_add(d->caption_display_status, (void*) gft, status);
}
*result = *status;
return 0;
}
static GtHMMERSingleHit* gt_hmmer_parse_status_get_hit(GtHMMERParseStatus *s,
GtUword i)
{
GtHMMERModelHit *mh;
gt_assert(s && s->models);
mh = gt_hashmap_get(s->models, gt_str_get(s->cur_model));
if (mh != NULL) {
if (s->strand == GT_STRAND_FORWARD) {
i += mh->last_array_size_fwd;
gt_assert(i < gt_array_size(mh->fwd_hits));
return *(GtHMMERSingleHit**) gt_array_get(mh->fwd_hits, i);
} else {
i += mh->last_array_size_rev;
gt_assert(i < gt_array_size(mh->rev_hits));
return *(GtHMMERSingleHit**) gt_array_get(mh->rev_hits, i);
}
} else return NULL;
}