// For ordered, the default should be 0 (if you just need to fill out the args)
// Note ONLY stable_id can be char, all other pk's must be IDType (see code)
Vector *BaseAdaptor_listDbIDs(BaseAdaptor *ba, char *table, char *pk, int ordered) {
int ok = 1;
char colName[1024];
if (pk == NULL) {
sprintf(colName, "%s_id", table);
} else {
strcpy(colName, pk);
}
char qStr[1024];
sprintf(qStr,"SELECT `%s` FROM `%s`", colName, table );
if ( BaseAdaptor_isMultiSpecies(BaseAdaptor *ba)
// For now just the multi species because I don't have adaptors in the Class hierarchy
// && $self->isa('Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor')
// && !$self->isa('Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor')
) {
char tmpStr[1024];
sprintf(tmpStr, "JOIN seq_region USING (seq_region_id) "
"JOIN coord_system cs USING (coord_system_id) "
"WHERE cs.species_id = "IDFMTSTR, BaseAdaptor_getSpeciesId(ba));
sprintf(qStr, "%s %s", qStr, tmpStr);
}
if (ordered) {
sprintf(qStr, "%s ORDER BY seq_region_id, seq_region_start", qStr);
}
StatementHandle *sth = ba->prepare(ba,qStr,strlen(qStr));
sth->execute(sth);
Vector *out = Vector_new();
if (strcmp(pk, "stable_id")) {
ResultRow *row;
while ((row = sth->fetchRow(sth))) {
char *stableId = row->getStringCopyAt(row, 0);
Vector_addElement(out, stableId);
}
} else {
IDType *idP;
ResultRow *row;
while ((row = sth->fetchRow(sth))) {
IDType id = row->getLongLongAt(row, 0);
if ((idP = calloc(1,sizeof(IDType))) == NULL) {
fprintf(stderr, "Failed allocating space for a id\n");
ok = 0;
} else {
*idP = id;
Vector_addElement(out, idP);
}
}
}
if (!ok) {
Vector_free(out);
out = NULL;
}
return out;
}
