static void tst5() {
params_ref ps;
nlsat::solver s(ps);
unsynch_mpq_manager & qm = s.qm();
anum_manager & am = s.am();
nlsat::pmanager & pm = s.pm();
nlsat::assignment as(am);
small_object_allocator allocator;
nlsat::interval_set_manager ism(am, allocator);
nlsat::evaluator ev(as, pm, allocator);
nlsat::var x0, x1;
x0 = pm.mk_var();
x1 = pm.mk_var();
polynomial_ref p(pm);
polynomial_ref _x0(pm), _x1(pm);
_x0 = pm.mk_polynomial(x0);
_x1 = pm.mk_polynomial(x1);
p = (_x0^2) + (_x1^2) - 2;
nlsat::poly * _p[1] = { p.get() };
bool is_even[1] = { false };
nlsat::bool_var b = s.mk_ineq_atom(nlsat::atom::GT, 1, _p, is_even);
nlsat::atom * a = s.bool_var2atom(b);
SASSERT(a != 0);
nlsat::interval_set_ref i(ism);
scoped_anum zero(am);
am.set(zero, 0);
as.set(0, zero);
i = ev.infeasible_intervals(a, true);
std::cout << "1) " << i << "\n";
as.set(1, zero);
i = ev.infeasible_intervals(a, true);
std::cout << "2) " << i << "\n";
}
static void tst4() {
enable_trace("nlsat_interval");
unsynch_mpq_manager qm;
anum_manager am(qm);
small_object_allocator allocator;
nlsat::interval_set_manager ism(am, allocator);
nlsat::interval_set_ref s1(ism), s2(ism), r(ism);
nlsat::literal l1(1, false);
nlsat::literal l2(2, false);
for (unsigned i = 0; i < 100; i++) {
s1 = mk_random(ism, am, 20, 3, 10, true, true, l1);
s2 = mk_random(ism, am, 20, 3, 10, true, true, l2);
r = tst_interval(s1, s2, 0, false);
check_subset_result(s1, s2, r, l1, l2);
}
for (unsigned i = 0; i < 100; i++) {
s1 = mk_random(ism, am, 200, 100, 20, true, true, l1);
s2 = mk_random(ism, am, 200, 100, 20, true, true, l2);
r = tst_interval(s1, s2, 0, false);
check_subset_result(s1, s2, r, l1, l2);
}
}
void
ClassRule::
readCRules(ECString path)
{
ECString flnm = path;
flnm += L"rules.txt";
ifstream is(flnm.c_str());
int wh = 2;
//wcerr << "RCR" << endl;
int modm = Term::stopTerm->toInt();
assert(is);
ECString tmp;
for( ; ; )
{
int d, m, r, t;
is >> tmp;
if(tmp == L"Thirds:")
{
wh = 3;
continue;
}
//wcerr << "T1 " << tmp << endl;
if(!is) break;
d = Term::get(tmp)->toInt();
is >> tmp;
m = Term::get(tmp)->toInt();
is >> r;
r--;
is >> tmp;
t = Term::get(tmp)->toInt();
assert(is);
ClassRule cr(d,m,r,t);
//wcerr << "RR " << cr << endl;
if(wh == 3) rBundles3_[d][m-modm].push_back(cr);
else rBundles2_[d][m-modm].push_back(cr);
}
flnm = path;
flnm += L"rules.m";
ifstream ism(flnm.c_str());
if(!ism) return;
ism >> tmp; // all thirds;
for( ; ; )
{
ECString tmp;
int d, m, t;
ism >> tmp;
//wcerr << "T1 " << tmp << endl;
if(!ism) break;
d = Term::get(tmp)->toInt();
ism >> tmp;
m = Term::get(tmp)->toInt();
ism >> tmp;
t = Term::get(tmp)->toInt();
assert(ism);
ClassRule cr(d,m,0,t);
rBundlesm_[d][m].push_back(cr);
}
}
boost::shared_ptr<TaskSlotAPI> Skill::
lookupSlot(std::string const & name)
{
shared_ptr<TaskSlotAPI> slot;
slot_map_t::iterator ism(slot_map_.find(name));
if (ism != slot_map_.end()) {
slot = ism->second;
}
return slot;
}
static void check_subset_result(nlsat::interval_set_ref const & s1,
nlsat::interval_set_ref const & s2,
nlsat::interval_set_ref const & r,
nlsat::literal l1,
nlsat::literal l2) {
nlsat::interval_set_manager ism(s1.m());
nlsat::interval_set_ref tmp(ism);
unsigned num = ism.num_intervals(r);
nlsat::literal_vector lits;
ism.get_justifications(r, lits);
SASSERT(lits.size() <= 2);
for (unsigned i = 0; i < num; i++) {
tmp = ism.get_interval(r, i);
ism.get_justifications(tmp, lits);
SASSERT(lits.size() == 1);
if (lits[0] == l1) {
SASSERT(ism.subset(tmp, s1));
}
else {
SASSERT(lits[0] == l2);
SASSERT(ism.subset(tmp, s2));
}
}
}
void WComboBox::findItemsites(int pItemID)
{
if (pItemID != -1)
{
QString iss("SELECT warehous_id, warehous_code, warehous_code "
"FROM site(), itemsite "
"WHERE ((itemsite_warehous_id=warehous_id)"
" AND (itemsite_item_id=<? value(\"itemid\") ?>) "
"<? if exists(\"active\") ?> AND (warehous_active) <? endif ?>"
"<? if exists(\"shipping\") ?>AND (warehous_shipping)<? endif ?>"
"<? if exists(\"transit\") ?>"
" AND (warehous_transit) "
"<? elseif exists(\"nottransit\") ?>"
" AND (NOT warehous_transit)"
"<? endif ?>"
"<? if exists(\"active\") ?> AND (itemsite_active) <? endif ?>"
"<? if exists(\"soldIS\") ?> AND (itemsite_sold) <? endif ?>"
"<? if exists(\"supplyIS\") ?> AND (itemsite_supply) <? endif ?>"
"<? if exists(\"inventory\") ?> AND (itemsite_controlmethod<>'N') <? endif ?>"
") "
"ORDER BY warehous_code;" );
ParameterList isp;
isp.append("itemid", pItemID);
switch (_type)
{
case AllActive:
isp.append("active");
break;
case AllActiveInventory:
isp.append("active");
isp.append("inventory");
break;
case NonTransit:
isp.append("nottransit");
isp.append("active");
break;
case Sold:
isp.append("active");
isp.append("nottransit");
isp.append("soldIS");
break;
/* TODO: ? previous version of this function didn't have Shipping case
case Shipping:
isp.append("shipping");
isp.append("active");
break;
*/
case Supply:
isp.append("active");
isp.append("supplyIS");
break;
case Transit:
isp.append("transit");
isp.append("active");
break;
case All:
default:
break;
}
MetaSQLQuery ism(iss);
XSqlQuery isq = ism.toQuery(isp);
populate(isq, ((_x_preferences) ?
_x_preferences->value("PreferredWarehouse").toInt() : -1));
if (currentItem() == -1)
setCurrentItem(0);
}
else
clear();
}
static void tst3() {
enable_trace("nlsat_interval");
unsynch_mpq_manager qm;
anum_manager am(qm);
small_object_allocator allocator;
nlsat::interval_set_manager ism(am, allocator);
scoped_anum sqrt2(am), m_sqrt2(am), two(am), m_two(am), three(am), one(am), zero(am);
am.set(two, 2);
am.set(m_two, -2);
am.set(one, 1);
am.root(two, 2, sqrt2);
am.set(m_sqrt2, sqrt2);
am.neg(m_sqrt2);
am.set(three, 3);
nlsat::literal p1(1, false);
nlsat::literal p2(2, false);
nlsat::literal p3(3, false);
nlsat::literal p4(4, false);
nlsat::literal np2(2, true);
nlsat::interval_set_ref s1(ism), s2(ism), s3(ism), s4(ism);
s1 = ism.mk_empty();
std::cout << "s1: " << s1 << "\n";
s2 = ism.mk(true, true, zero, false, false, sqrt2, np2);
std::cout << "s2: " << s2 << "\n";
s3 = ism.mk(false, false, zero, false, false, two, p1);
std::cout << "s3: " << s3 << "\n";
s4 = ism.mk_union(s2, s3);
std::cout << "s4: " << s4 << "\n";
// Case
// s1: [ ... ]
// s2: [ ... ]
s1 = ism.mk(false, false, zero, false, false, two, p1);
s2 = ism.mk(false, false, zero, false, false, two, p2);
tst_interval(s1, s2, 1);
// Case
// s1: [ ... ]
// s2: [ ... ]
s1 = ism.mk(false, false, zero, false, false, two, p1);
s2 = ism.mk(false, false, m_sqrt2, false, false, one, p2);
s3 = ism.mk_union(s1, s2);
tst_interval(s1, s2, 2);
// Case
// s1: [ ... ]
// s2: [ ... ]
s1 = ism.mk(false, false, m_sqrt2, false, false, one, p1);
s2 = ism.mk(false, false, zero, false, false, two, p2);
tst_interval(s1, s2, 2);
// Case
// s1: [ ... ]
// s2: [ ... ]
s1 = ism.mk(false, false, m_sqrt2, false, false, one, p1);
s2 = ism.mk(false, false, two, false, false, three, p2);
tst_interval(s1, s2, 2);
// Case
// s1: [ ... ]
// s2: [ ... ]
s1 = ism.mk(false, false, m_sqrt2, false, false, three, p1);
s2 = ism.mk(false, false, zero, false, false, two, p2);
tst_interval(s1, s2, 1);
// Case
// s1: [ ... ]
// s2: [ ... ] [ ... ]
s1 = ism.mk(false, false, m_two, false, false, two, p1);
s2 = ism.mk(false, false, m_sqrt2, false, false, zero, p2);
s3 = ism.mk(false, false, one, false, false, three, p2);
s2 = ism.mk_union(s2, s3);
tst_interval(s1, s2, 2);
// Case
// s1: [ ... ]
// s2: [ ... ]
s1 = ism.mk(false, false, m_two, false, false, two, p1);
s2 = ism.mk(false, false, two, false, false, three, p2);
tst_interval(s1, s2, 2);
s2 = ism.mk(true, false, two, false, false, three, p2);
tst_interval(s1, s2, 2);
s2 = ism.mk(true, false, two, false, false, three, p1);
tst_interval(s1, s2, 1);
s1 = ism.mk(false, false, m_two, true, false, two, p1);
tst_interval(s1, s2, 2);
s1 = ism.mk(false, false, two, false, false, two, p1);
s2 = ism.mk(false, false, two, false, false, three, p2);
tst_interval(s1, s2, 1);
// Case
// s1: [ ... ] [ ... ]
// s2: [ .. ] [ ... ] [ ... ]
s1 = ism.mk(false, false, m_two, false, false, zero, p1);
s3 = ism.mk(false, false, one, false, false, three, p1);
s1 = ism.mk_union(s1, s3);
s2 = ism.mk(true, true, zero, false, false, m_sqrt2, p2);
tst_interval(s1, s2, 3);
s3 = ism.mk(false, false, one, false, false, sqrt2, p2);
s2 = ism.mk_union(s2, s3);
s3 = ism.mk(false, false, two, true, true, zero, p2);
s2 = ism.mk_union(s2, s3);
tst_interval(s1, s2, 4);
// Case
s1 = ism.mk(true, true, zero, false, false, one, p1);
s2 = ism.mk(true, false, one, true, true, zero, p2);
tst_interval(s1, s2, 2);
s2 = ism.mk(true, false, one, false, false, two, p2);
s3 = ism.mk(false, false, two, true, true, zero, p1);
s2 = ism.mk_union(s2, s3);
tst_interval(s1, s2, 3);
}
// void test() {
//
// aligned_buffer<short> a(16);
// aligned_buffer<short> b(16);
// aligned_buffer<short> c(16);
//
// std::fill( a.begin(), a.end(), 1 );
// std::fill( b.begin(), b.end(), 2 );
// a.m_ptr[0] = 2;
//
// typedef vector_unit<short,16> vu;
//
// vu::vec_t av = vu::load(a.m_ptr);
// vu::vec_t bv = vu::load(b.m_ptr);
//
// vu::store( vu::cmp_lt(av,bv), c.m_ptr );
//
// for( int i = 0; i < c.size(); i++ ) {
//
// std::cout << i << ": " << c.m_ptr[i] << "\n";
// }
//
// }
int main( int argc, char *argv[] ) {
// test();
// return 0;
seqs sq;
seqs sd;
// typedef mapped_file file_input;
typedef std::ifstream file_input;
if( argc != 6 ) {
throw std::runtime_error( "missing parameters. expect: <open> <ext> <query.fa> <db.fa> <matrix>" );
}
const int gap_open = atoi( argv[1] );
const int gap_extend = atoi( argv[2] );
//std::cout << "gap: " <<
std::ifstream ism( argv[5] );
scoring_matrix sm( ism );
file_input qfi( argv[3] );
inc_fasta<file_input, scoring_matrix> qfasta( qfi, sm );
file_input dfi( argv[4] );
inc_fasta<file_input, scoring_matrix> dfasta( dfi, sm );
// for( int i = 0 ; i < sd.names.size(); i++ ) {
// int sc = align<int>( sd.data[i], sq.data[0], sm );
// std::cout << sc << "\t" << sd.names[i] << "\n";
// }
#if 0
const int W = 8;
typedef short score_t;
typedef short sscore_t;
#else
const int W = 16;
typedef unsigned char score_t;
typedef char sscore_t;
#endif
persistent_state<score_t> ps;
// size_t db_size = (sd.names.size() / W ) * W;
#ifndef LOCAL_ALIGN
#define PAD_FRONT
#endif
typedef uint8_t seq_char_t;
std::string dname[W];
std::vector<seq_char_t> ddata[W];
// size_t dpad[W];
aligned_buffer<seq_char_t> ddata_int;
// std::vector<score_t> dmask[W];
std::string qname;
std::vector<seq_char_t> qdata;
bool have_input = true;
size_t n_qseq = 0;
size_t n_qchar = 0;
size_t n_dseq = 0;
size_t n_dchar = 0;
bool first_block = true;
while( have_input ) {
size_t maxlen = 0;
int lj = -1;
// determine db sequences for the current block
for( int j = 0; j < W; j++ ) {
dname[j].resize(0);
ddata[j].resize(0);
have_input = dfasta.next_seq( dname[j], ddata[j] );
// if there aren't enough db sequences left to fill the block, pad with last db sequence
if( !have_input ) {
// break immediately if there are no db sequences left (means #db-seqs % W == 0, or otherwise have_input would have been == false from last iteration)
if( j == 0 ) {
break;
} else {
dname[j] = dname[lj];
ddata[j] = ddata[lj];
}
} else {
n_dseq++;
n_dchar += ddata[j].size();
lj = j; // store largest valid 'j'
// for( int i = 0; i < ddata[j].length(); i++ ) {
//
// ddata[j][i] = sm.state_backmap(ddata[j][i]);
// }
}
// dmask[j].clear();
// dmask[j].resize(ddata[j].length(), 0xffff );
maxlen = std::max( maxlen, ddata[j].size() );
}
// jf == -1 at this point means that the block is empty (#db-seqs % W == 0)
if( lj == -1 ) {
break;
}
// WARNING: front-padding is currently defunct
#ifdef PAD_FRONT
for( int j = 0; j < W; j++ ) {
dpad[j] = maxlen - ddata[j].size();
}
#endif
// lj == -1 means that there are no remaining sequences
// std::cout << "sdis: " << sdi.size() << "\n";
aligned_buffer<sscore_t> qprofile( maxlen * W * sm.num_states());
aligned_buffer<sscore_t>::iterator qpi = qprofile.begin();
#if 0
for( int j = 0; j < sm.num_states(); j++ ) {
const int jstate = sm.get_state(j);
// const scoring_matrix::score_t *slice = sm.get_slice(jstate);
const scoring_matrix::score_t *cslice = sm.get_cslice(j);
for( int k = 0; k < maxlen; k++ ) {
for( int l = 0; l < W; l++ ) {
std::vector<seq_char_t> &sdi = ddata[l];
#ifdef PAD_FRONT
const size_t frontpad = dpad[l];//maxlen - sdi.size();
//if( k < sdi.size() ) {
if( k >= frontpad ) {
//*qpi = sm.get_score( sdi[k], jstate);
*qpi = cslice[sdi[k - frontpad]];
#else
if( k < sdi.size() ) {
// *qpi = slice[sdi[k]];
*qpi = cslice[sdi[k]];
#endif
} else {
*qpi = 0;
}
// std::cout << "prof: " << (qpi - qprofile.begin() ) << " " << *qpi << " " << int(j) << " " << char(sm.get_state(j)) << " " << sdi[k] << "\n";
qpi++;
}
}
}
#else
// setup the qprofile (= lookup table for match penalties along the db-sequences in the current block)
// this is the faster (at least on core i5) two-step version, using interleaved db-sequences
// setup buffer for interleaved db sequences
if( ddata_int.size() < maxlen * W ) {
ddata_int.resize(maxlen * W);
}
// copy individual db sequences into interleaved buffer (padding the shorter sequnences
aligned_buffer<seq_char_t>::iterator dint_iter = ddata_int.begin();
const int zero_state = sm.get_zero_state();
for( size_t i = 0; i < maxlen; i++ ) {
for( int j = 0; j < W; j++ ) {
std::vector<seq_char_t> &sdi = ddata[j];
if( i < sdi.size() ) {
*dint_iter = sdi[i];
} else {
*dint_iter = zero_state;
}
++dint_iter;
}
}
for( size_t j = 0; j < sm.num_states(); j++ ) {
dint_iter = ddata_int.begin();
const char *cslice = sm.get_cslice(j);
for( size_t k = 0; k < maxlen; k++ ) {
for( int l = 0; l < W; l++ ) {
// if( *dint_iter == zero_state ) {
// std::cout << int(cslice[*dint_iter]) << "\n";
//
// }
*qpi = cslice[*dint_iter];
++dint_iter;
++qpi;
}
}
}
#endif
// std::cout << "sdis2: " << sdi.size() << std::endl;
// aligned_buffer<short> dv(sdi.size() * W);
// short *dv_iter = dv.begin();
//
// for( int j = 0; j < sdi.size(); j++ ) {
//
// for( int k = 0; k < W; k++ ) {
// *dv_iter = sdi[j];
// dv_iter++;
// }
//
// }
// aligned_buffer<score_t> len(W);
// for( int j = 0; j < W; j++ ) {
// len.m_ptr[j] = sd.data[i + j].size();
// }
std::vector<int> out(W);
qfasta.reset();
while( qfasta.next_seq( qname, qdata )) {
if( first_block ) {
n_qseq++;
n_qchar+=qdata.size();
}
align_vec<score_t,sscore_t,W>( ps, maxlen, qdata, sm, qprofile, gap_open, gap_extend, out );
for( int j = 0; j <= lj; j++ ) {
// std::cout << out[j] << "\t" << dname[j] << " " << qname << " " << ddata[j].size() << "\n";
std::cout << out[j] << "\t" << dname[j] << "\n";
}
qname.resize(0);
qdata.resize(0);
}
first_block = false;
}
std::cerr << n_qseq << "[" << n_qchar << "] x " << n_dseq << "[" << n_dchar << "]\n";
}
