deriv_note_ptr
parse(string const& str)
{
boost::smatch m;
span_t span;
int synid;
string tok;
score_t total, inside;
if (regex_match(str,m,synre)) {
total = score_t(boost::lexical_cast<float>(m.str(1)),as_neglog10());
inside = score_t(boost::lexical_cast<float>(m.str(2)),as_neglog10());
span = span_t(boost::lexical_cast<int>(m.str(3)),boost::lexical_cast<int>(m.str(4)));
synid = boost::lexical_cast<int>(m.str(5));
return deriv_note_ptr(new deriv_note(span,synid,total,inside));
} else if (regex_match(str,m,virtre)) {
total = score_t(boost::lexical_cast<float>(m.str(1)),as_neglog10());
inside = score_t(boost::lexical_cast<float>(m.str(2)),as_neglog10());
span = span_t(boost::lexical_cast<int>(m.str(3)),boost::lexical_cast<int>(m.str(4)));
tok = m.str(5);
return deriv_note_ptr(new deriv_note(span,tok,total,inside));
}
else {
throw runtime_error("in parse_error module: could not parse "+str);
}
}
virtual void finalize()
{
indexed_token_factory &tf = base_t::gram.dict();
filt->finalize();
while (not filt->empty()) {
typename base_t::edge_equiv_type eq = filt->top();
insert(kept_edges, eq.representative(), true);
edge_q.push_back(eq);
filt->pop();
}
test_func.reset(all_edges.begin(), all_edges.end());
edge_iterator itr = all_edges.begin();
edge_iterator end = all_edges.end();
for (; itr != all_edges.end(); ++itr) {
edge_iterator pos = kept_edges.find(*itr);
bool should_keep = test_func(*itr);
bool did_keep = (pos != kept_edges.end());
if (did_keep) {
assert(max(pos->score(),itr->score())/min(pos->score(),itr->score())
< score_t(1.0 + 1e-5));
}
if (should_keep != did_keep) {
std::cout << "ERROR: filtering mistake: edge: "
<< print(*itr,tf) << "expected to be kept? "
<< (should_keep?"true":"false") << std::endl;
}
}
}
score_t align( std::string &a, std::string &b, scoring_matrix &m ) {
std::vector<score_t> s( a.size());
std::vector<score_t> si( a.size());
std::fill( s.begin(), s.end(), 0 );
std::fill( si.begin(), si.end(), 0 );
const score_t SMALL = -32000;
score_t max = SMALL;
for( int ib = 0; ib < b.size(); ib++ ) {
char bc = b[ib];
score_t last_sl = SMALL;
score_t last_sc = 0;
score_t last_sdiag = 0;
for( int ia = 0; ia < a.size(); ia++ ) {
char ac = a[ia];
score_t match = m.get_score( ac, bc );
score_t sm = last_sdiag + match;
const score_t GAP_EXT = -1;
const score_t GAP_OPEN = -2;
score_t sl = last_sl + GAP_EXT;
sl = std::max( sl, score_t(last_sc + GAP_OPEN) );
last_sl = sl;
last_sdiag = s[ia];
score_t su = si[ia] + GAP_EXT;
su = std::max( su, score_t(last_sdiag + GAP_OPEN) );
si[ia] = su;
score_t sc = std::max( sm , std::max( std::max( sl, su ), score_t(0) ) );
s[ia] = sc;
last_sc = sc;
max = std::max( sc, max );
}
}
return max;
}
