void tex::append_choices ()
{
tail_append(new_choice());
incr(save_ptr);
saved(-1) = 0;
scan_left_brace();
push_math(MATH_CHOICE_GROUP);
}
void GapFiller::BFS(const CondensedDeBruijnGraph& graph, const size_t from, const size_t to, int gap, size_t max_depth, size_t max_queue, PathList& pathlist) {
size_t step = 0;
Path path = boost::assign::list_of(from);
typedef std::pair< Path, int > Choice;
std::deque< Choice > Q = boost::assign::list_of(std::make_pair(
path, 0 - (_K - 1)
));
while (!Q.empty()) {
++step;
if (step > max_depth) {
LOG4CXX_DEBUG(logger, boost::format("BFS step is bigger than %d...") % max_depth);
break;
}
if (Q.size() > max_queue) {
LOG4CXX_DEBUG(logger, boost::format("BFS Q size=%d is greater than %d...") % Q.size() % max_queue);
break;
}
std::deque< Choice > nextQ;
while (!Q.empty()) {
Choice choice = Q.front();
Q.pop_front();
size_t node = choice.first.back();
if (node == to) {
pathlist.push_back(choice.first);
}
if (choice.second > gap - (_K - 1)) {
continue;
}
const CondensedDeBruijnGraph::CondensedEdge& edge = graph._indexer[node];
std::string suffix = edge.seq.substr(edge.seq.length() - (_K - 1), _K - 1);
CondensedDeBruijnGraph::NodeList::const_iterator i = graph._parents.find(suffix);
if (i != graph._parents.end()) {
for (CondensedDeBruijnGraph::EdgeList::const_iterator j = i->second.begin(); j != i->second.end(); ++j) {
//size_t length = graph._indexer[j->second].seq.length();
size_t length = graph._indexer[j->second].seq.length() - (_K - 1);
Choice new_choice(choice);
new_choice.first.push_back(j->second);
new_choice.second += length;
nextQ.push_back(new_choice);
}
}
}
Q = nextQ;
}
}
/**
* append_char_choice
*
* Create a new choice record. Store the string value in a safe place.
* Add the new choice record to the list.
*
* NB - This is only used by matchers, so permuter is always NO_PERM
* SPC 16/9/92
*/
CHOICES append_char_choice(CHOICES ratings,
const char *string,
const char *lengths,
float rating,
float certainty,
inT8 config,
int script_id) {
A_CHOICE *this_choice;
this_choice = new_choice (string, lengths, rating, certainty,
config, script_id, NO_PERM, false, NULL);
ratings = push_last (ratings, (LIST) this_choice);
return (ratings);
}
/**
* copy_choices
*
* Copy a list of choices. This means that there will be two copies
* in memory.
*/
CHOICES copy_choices(CHOICES choices) {
CHOICES l;
CHOICES result = NIL;
iterate_list(l, choices) {
A_CHOICE *choice = (A_CHOICE *)(first_node(l));
result = push (result,
(LIST) new_choice (class_string(choice),
class_lengths(choice),
class_rating(choice),
class_certainty(choice),
class_config(choice),
class_script_id(choice),
class_permuter(choice),
class_fragment_mark(choice),
class_fragment_lengths(choice)));
}
