/* Create a category map with a category for each feature type in a
GFF_Set. Category numbers are assigned in order of appearance of
types */
CategoryMap* cm_new_from_features(GFF_Set *feats) {
int i;
CategoryMap *retval;
Hashtable *hash;
List *types;
/* first scan features for all types */
hash = hsh_new(10);
types = lst_new_ptr(10);
for (i = 0; i < lst_size(feats->features); i++) {
GFF_Feature *f = lst_get_ptr(feats->features, i);
checkInterruptN(i, 10000);
if (hsh_get(hash, f->feature->chars) == (void*)-1) {
lst_push_ptr(types, f->feature);
hsh_put_int(hash, f->feature->chars, 1);
}
}
hsh_free(hash);
/* now create a simple category map */
retval = cm_new(lst_size(types));
for (i = 0; i <= retval->ncats; i++) {
String *type = i == 0 ? str_new_charstr(BACKGD_CAT_NAME) :
str_dup(lst_get_ptr(types, i-1));
retval->ranges[i] = cm_new_category_range(type, i, i);
}
lst_free(types);
return retval;
}
/* Closes all outfiles. If already closed, reopen with append, add #eof
closer, and close again. see comment above at get_outfile */
void close_outfiles(List *outfileList, Hashtable *outfileHash) {
List *keys = hsh_keys(outfileHash);
int *done, idx, i;
char *fname;
FILE *outfile;
done = smalloc(lst_size(keys)*sizeof(int));
for (i=0; i<lst_size(keys); i++) {
done[i]=0;
fname = (char*)lst_get_ptr(keys, i);
idx = hsh_get_int(outfileHash, fname);
outfile = (FILE*)lst_get_ptr(outfileList, idx);
if (outfile != NULL) {
mafBlock_close_outfile(outfile);
done[i]=1;
}
}
for (i=0; i<lst_size(keys); i++) {
if (done[i]) continue;
fname = (char*)lst_get_ptr(keys, i);
outfile = phast_fopen(fname, "a");
mafBlock_close_outfile(outfile);
}
sfree(done);
lst_free(keys);
lst_free(outfileList);
hsh_free(outfileHash);
}
void
rb_config_free()
{
hsh_free(g_state.poll_by_key);
/* Note that rb_item's are owned by pollers */
free_pollers(g_state.polls);
}
//frees all elements of block except prev and next pointers
void mafBlock_free(MafBlock *block) {
if (block->aLine != NULL) {
str_free(block->aLine);
block->aLine = NULL;
}
if (block->specMap != NULL) {
hsh_free(block->specMap);
block->specMap = NULL;
}
mafBlock_free_data(block);
sfree(block);
}
void mafBlock_reorder(MafBlock *block, List *specNameOrder) {
String *str;
MafSubBlock *sub;
List *newData;
Hashtable *newSpecMap;
int i, idx, *found, oldSize = lst_size(block->data), newSize = lst_size(specNameOrder);
found = smalloc(oldSize*sizeof(int));
for (i=0; i<oldSize; i++) found[i]=0;
newData = lst_new_ptr(oldSize);
newSpecMap = hsh_new(100);
for (i=0; i<newSize; i++) {
str = (String*)lst_get_ptr(specNameOrder, i);
idx = hsh_get_int(block->specMap, str->chars);
if (idx != -1) {
if (found[idx]==1) die("ERROR: species %s appears twice in reorder list\n",
str->chars);
sub = (MafSubBlock*)lst_get_ptr(block->data, idx);
hsh_put_int(newSpecMap, sub->src->chars, lst_size(newData));
hsh_put_int(newSpecMap, sub->specName->chars, lst_size(newData));
lst_push_ptr(newData, (void*)sub);
found[idx] = 1;
}
}
for (i=0; i<oldSize; i++) {
if (found[i]==0) {
sub = (MafSubBlock*)lst_get_ptr(block->data, i);
mafSubBlock_free(sub);
}
}
hsh_free(block->specMap);
lst_free(block->data);
block->specMap = newSpecMap;
block->data = newData;
sfree(found);
}
