int main ()
{
Stock st1( "Company A", 5.12 );
Stock st2( "Company B", 7.13 );
Stock st3( "Company C", 50.00 );
StockLogger logger( std::cout );
st1.addChangeListener( logger );
st2.addChangeListener( logger );
BiggestChangeRecorder recorder;
st1.addChangeListener( recorder );
st2.addChangeListener( recorder );
StockChangeImportanceFilter filteredLogger( 10.00, logger );
StockChangeImportanceFilter filteredRecorder( 20.00, recorder );
st3.addChangeListener( filteredLogger );
st3.addChangeListener( filteredRecorder );
st1.updatePrice( 6.21 );
st2.updatePrice( 7.09 );
st1.updatePrice( 6.01 );
st3.updatePrice( 55.00 );
st3.updatePrice( 44.00 );
std::cout << "Biggest positive change : "
<< recorder.getMaxPositiveChange ()
<< std::endl;
std::cout << "Biggest negative change : "
<< recorder.getMaxNegativeChange ()
<< std::endl;
}
TEST(BaseCluster, Read)
{
std::stringstream input;
tawara::UIntElement tc(tawara::ids::Timecode, 42);
tawara::UIntElement st1(tawara::ids::SilentTrackNumber, 1);
tawara::UIntElement st2(tawara::ids::SilentTrackNumber, 2);
tawara::UIntElement ps(tawara::ids::PrevSize, 0x1234);
FakeCluster e;
std::streamsize body_size(tc.size());
tawara::vint::write(body_size, input);
tc.write(input);
EXPECT_EQ(tawara::vint::size(body_size) + body_size,
e.read(input));
EXPECT_EQ(42, e.timecode());
EXPECT_TRUE(e.silent_tracks().empty());
EXPECT_EQ(0, e.previous_size());
body_size += tawara::ids::size(tawara::ids::SilentTracks) +
tawara::vint::size(st1.size() + st2.size()) +
st1.size() + st2.size() + ps.size();
tawara::vint::write(body_size, input);
tc.write(input);
tawara::ids::write(tawara::ids::SilentTracks, input);
tawara::vint::write(st1.size() + st2.size(), input);
st1.write(input);
st2.write(input);
ps.write(input);
EXPECT_EQ(tawara::vint::size(body_size) + body_size,
e.read(input));
EXPECT_EQ(42, e.timecode());
EXPECT_FALSE(e.silent_tracks().empty());
EXPECT_EQ(0x1234, e.previous_size());
// Body size value wrong (too small)
input.str(std::string());
tawara::vint::write(2, input);
tc.write(input);
ps.write(input);
EXPECT_THROW(e.read(input), tawara::BadBodySize);
// Invalid child
input.str(std::string());
tawara::UIntElement ue(tawara::ids::EBML, 0xFFFF);
tawara::vint::write(ue.size(), input);
ue.write(input);
EXPECT_THROW(e.read(input), tawara::InvalidChildID);
// Missing timecode
input.str(std::string());
tawara::vint::write(ps.size(), input);
ps.write(input);
EXPECT_THROW(e.read(input), tawara::MissingChild);
}
void SAMLTokenTest::TestSAML2Token() {
Arc::SOAPEnvelope soap1(xml);
CPPUNIT_ASSERT((bool)soap1);
Arc::SAMLToken st1(soap1, certfile, keyfile, Arc::SAMLToken::SAML2);
CPPUNIT_ASSERT((bool)st1);
std::string str;
st1.GetXML(str);
Arc::SOAPEnvelope soap2(str);
CPPUNIT_ASSERT((bool)soap2);
Arc::SAMLToken st2(soap2);
CPPUNIT_ASSERT((bool)st2);
CPPUNIT_ASSERT(st2.Authenticate());
CPPUNIT_ASSERT(st2.Authenticate("../../credential/test/ca_cert.pem", ""));
}
// ============================================================================
// the main execution method
// ============================================================================
StatusCode GaudiExamples::StatSvcAlg::execute ()
{
Stat st1 ( m_stat , "counter1" ) ;
Stat st2 ( m_stat , "counter2" ) ;
Stat st3 ( m_stat , "counter3" , 0.3 ) ;
Stat eff ( m_stat , "eff" , 0 < sin( 10 * st1->flag() ) ) ;
//
st1 += 0.1 ;
st1 -= 0.1000452 ;
st2 += st1 ;
++st3 ;
st2-- ;
eff += 0 < cos ( 20 * st2->flag() ) ;
//
return StatusCode::SUCCESS ;
}
size_t SQLiteBundleSet::Factory::__create(SQLiteDatabase &db, const std::string &name, bool persistent) throw (SQLiteDatabase::SQLiteQueryException)
{
// create a new name (fails, if the name already exists)
SQLiteDatabase::Statement st1(db._database, SQLiteDatabase::_sql_queries[SQLiteDatabase::BUNDLE_SET_NAME_ADD]);
sqlite3_bind_text(*st1, 1, name.c_str(), static_cast<int>(name.length()), SQLITE_TRANSIENT);
sqlite3_bind_int(*st1, 2, persistent ? 1 : 0);
st1.step();
// get the ID of the name
SQLiteDatabase::Statement st2(db._database, SQLiteDatabase::_sql_queries[SQLiteDatabase::BUNDLE_SET_NAME_GET_ID]);
sqlite3_bind_text(*st2, 1, name.c_str(), static_cast<int>(name.length()), SQLITE_TRANSIENT);
sqlite3_bind_int(*st2, 2, persistent ? 1 : 0);
if (st2.step() == SQLITE_ROW) {
return sqlite3_column_int64(*st2, 0);
}
throw SQLiteDatabase::SQLiteQueryException("could not create the bundle-set name");
}
TEST(BaseCluster, Size)
{
FakeCluster e;
tawara::UIntElement tc(tawara::ids::Timecode, 0);
std::streamsize body_size(tc.size());
EXPECT_EQ(tawara::ids::size(tawara::ids::Cluster) + 8 + body_size, e.size());
tawara::UIntElement st1(tawara::ids::SilentTrackNumber, 1);
tawara::UIntElement st2(tawara::ids::SilentTrackNumber, 2);
body_size += tawara::ids::size(tawara::ids::SilentTracks) +
tawara::vint::size(st1.size() + st2.size()) +
st1.size() + st2.size();
e.silent_tracks().push_back(tawara::SilentTrackNumber(1));
e.silent_tracks().push_back(tawara::SilentTrackNumber(2));
EXPECT_EQ(tawara::ids::size(tawara::ids::Cluster) + 8 + body_size, e.size());
tawara::UIntElement ps(tawara::ids::PrevSize, 0x1234);
body_size += ps.size();
e.previous_size(0x1234);
EXPECT_EQ(tawara::ids::size(tawara::ids::Cluster) + 8 + body_size, e.size());
}
TEST(BaseCluster, Write)
{
std::ostringstream output;
std::stringstream expected;
tawara::UIntElement tc(tawara::ids::Timecode, 0);
tawara::UIntElement st1(tawara::ids::SilentTrackNumber, 1);
tawara::UIntElement st2(tawara::ids::SilentTrackNumber, 2);
tawara::UIntElement ps(tawara::ids::PrevSize, 0x1234);
FakeCluster e;
std::streamsize expected_size(tc.size());
tawara::ids::write(tawara::ids::Cluster, expected);
tawara::vint::write(expected_size, expected, 8);
tc.write(expected);
EXPECT_EQ(tawara::ids::size(tawara::ids::Cluster) + 8 + expected_size,
e.write(output));
EXPECT_PRED_FORMAT2(test_utils::std_buffers_eq, output.str(),
expected.str());
expected_size += tawara::ids::size(tawara::ids::SilentTracks) +
tawara::vint::size(st1.size() + st2.size()) +
st1.size() + st2.size() + ps.size();
e.silent_tracks().push_back(tawara::SilentTrackNumber(1));
e.silent_tracks().push_back(tawara::SilentTrackNumber(2));
e.previous_size(0x1234);
output.str(std::string());
expected.str(std::string());
tawara::ids::write(tawara::ids::Cluster, expected);
tawara::vint::write(expected_size, expected, 8);
tc.write(expected);
tawara::ids::write(tawara::ids::SilentTracks, expected);
tawara::vint::write(st1.size() + st2.size(), expected);
st1.write(expected);
st2.write(expected);
ps.write(expected);
EXPECT_EQ(tawara::ids::size(tawara::ids::Cluster) + 8 + expected_size,
e.write(output));
EXPECT_PRED_FORMAT2(test_utils::std_buffers_eq, output.str(),
expected.str());
}
// wyciaga informacje z lini textu z pliku
void ConfFile::parse()
{
string t;
while (getline(cFile, t))
{
if (t.size() == 0)
continue;
istringstream st1(t);
char c;
st1 >> c;
if (c == '#')
continue;
int t1 = t.find("=");
t.replace(t1, 1, " ");
istringstream st2(t);
string v;
string lab;
st2 >> lab >> v;
mLabels[lab] = v;
};
}
int sc_main(int ac, char *av[])
{
sc_fifo<int> st1("ST1", 2), st2("ST2", 2);
sc_fifo<int> a1("A1", 2), a2("A2", 2), a3("A3", 2);
sc_fifo<int> b1("B1", 2), b2("B2", 2), b3("B3", 2);
sc_clock clock("CLOCK");
sawtooth ST("TB1", clock, st1, st2);
delay D1("D1", clock, st1, a1);
downsample DN1("DN1", clock, a1, a2);
upsample UP1("UP1", clock, a2, a3);
downsample DN2("DN2", clock, st2, b1);
upsample UP2("UP2", clock, b1, b2);
delay D2("D2", clock, b2, b3);
adder A ("A", clock, a3, b3);
sc_start(100, SC_NS);
return 0;
}
void prepare_data(string filename)
{/*{{{*/
// create defect center
double x = 0.0, y = 0.0, z = 0.89175;
vec coord; coord << x << y << z;
NVCenter nv(NVCenter::N14, coord);
double magBx = 0.0, magBy = 0.0, magBz = 1e-5;
nv.set_magB(magBx, magBy, magBz);
nv.make_espin_hamiltonian();
cout << nv.get_eigen_state(0) << endl;
cout << nv.get_eigen_state(1) << endl;
cSPIN espin=nv.get_espin();
PureState st0(nv.get_eigen_state(0));
PureState st1(nv.get_eigen_state(1));
espin.set_coordinate(coord);
cout << "espin coordinate = " << espin.get_coordinate() << endl;
// create bath spins
cSpinSourceFromFile spin_file(filename);
cSpinCollection spins(&spin_file);
spins.make();
vector<cSPIN> sl = spins.getSpinList();
cout << sl[0].get_coordinate() << sl[0].get_gamma() << endl;
cout << sl[1].get_coordinate() << sl[1].get_gamma() << endl;
vec magB; magB << magBx << magBy << magBz;
SpinZeemanInteraction zee(sl, magB);
SpinDipolarInteraction dip(sl);
DipolarField hf_field0(sl, espin, st0);
DipolarField hf_field1(sl, espin, st1);
Hamiltonian hami0(sl);
hami0.addInteraction(zee);
hami0.addInteraction(dip);
hami0.addInteraction(hf_field0);
hami0.make();
Hamiltonian hami1(sl);
hami1.addInteraction(zee);
hami1.addInteraction(dip);
hami1.addInteraction(hf_field1);
hami1.make();
cout << hami0.getMatrix() << endl;
cout << hami1.getMatrix() << endl;
Liouvillian lv0(hami0, SHARP);
Liouvillian lv1(hami1, FLAT);
Liouvillian lvH = lv0 - lv1;
double rate = 2.0*datum::pi*1e4;
vec axis; axis << 1.0 << 1.0 << 1.0;
SpinDephasing dephasing(sl, rate, normalise(axis));
LiouvilleSpaceOperator dephaseOperator(sl);
dephaseOperator.addInteraction(dephasing);
dephaseOperator.make();
QuantumOperator lv = lvH + dephaseOperator;
lv.saveMatrix("lv");
vec _bath_polarization = zeros<vec>(3);
SpinPolarization p(sl, _bath_polarization);
DensityOperator ds(sl);
ds.addStateComponent(p);
ds.make();
ds.makeVector();
cout << ds.getVector() << endl;
cout << ds.getMatrix() << endl;
}/*}}}*/
//this constructor parses the input to get separated terms and add them to List_Terms
Polynomial::Polynomial(string& poly)
{
//temporary variables to store the term, the coefficient and the exponent
int expo = 0;
int coef = 0;
string coefSt;
string expoSt;
string currentTerm;
// replace - with +-
ReplaceStringInPlace (poly,string("-"),string("+-"));
// split input by + to get separated terms
String_Tokenizer st1(poly, "+");
// continue to parse as long as there is a term
while (st1.has_more_tokens())
{
currentTerm = trim(st1.next_token()); // get current Term
if (currentTerm.find("x^") != string::npos) // term contains "x^"
{
string first_Token, second_Token; // variables to store the coefficient and the exponent
// split currentTerm by x^
String_Tokenizer st2(currentTerm, "x^");
first_Token = trim(st2.next_token());
second_Token = trim(st2.next_token());
if (currentTerm.find(first_Token) < currentTerm.find("x^") ) // first_Token is the coefficient
{
if (first_Token == "-") //special case (user entered "-x^...")
coefSt = "-1";
else
coefSt = first_Token;
expoSt = second_Token != "" ? second_Token : throw invalid_argument( "Invalid Input" ); // only assign the exponent if second_Token is not empty
}
else if (currentTerm.find(first_Token) > currentTerm.find("x^") ) // first_Token is the exponent (the coefficient is hidden with value 1 )
{
coefSt = "1";
expoSt = first_Token;
}
else throw invalid_argument( "Invalid Input" );
}
else if (currentTerm.find("x") != string::npos) // term contains "x"
{
//split currentTerm by x
String_Tokenizer st2(currentTerm, "x");
if (!st2.has_more_tokens()) // the term is "x" only
{
coefSt = "1";
expoSt = "1";
}
else // the term has a coefficient
{
coefSt = trim(st2.next_token());
if (coefSt == "-") //special case (user entered "-x...")
coefSt = "-1";
expoSt = "1";
}
}
else if (currentTerm.find("X") != string::npos) // term contains "X" uppercase
throw invalid_argument( "Invalid Input" );
else // term contains only the coefficient
{
coefSt = currentTerm;
expoSt = "0";
}
//convert string to int
coef= stoi(coefSt);
expo=stoi(expoSt);
//create the term and add to the list only if the coefficient is not 0
if (coef != 0)
List_Terms.push_back(Term(coef,expo));
}
}
int main(void)
{
FragTrap ft1("Alf");
FragTrap ft2("Bob");
FragTrap ft3(ft1);
std::cout << std::endl;
ft3 = ft2;
std::cout << std::endl;
ft1.rangedAttack("Bob");
std::cout << std::endl;
ft1.meleeAttack("Bob");
std::cout << std::endl;
ft1.takeDamage(3);
std::cout << std::endl;
ft1.beRepaired(3);
std::cout << std::endl;
ft1.takeDamage(1000);
std::cout << std::endl;
ft1.beRepaired(1000);
std::cout << std::endl;
ft1.beRepaired(3);
std::cout << std::endl;
ft1.Ep = 100;
std::cout << std::endl;
ft1.vaulthunter_dot_exe("1");
ft1.vaulthunter_dot_exe("2");
ft1.vaulthunter_dot_exe("3");
ft1.vaulthunter_dot_exe("4");
ft1.vaulthunter_dot_exe("5");
std::cout << std::endl;
ScavTrap st1("John");
ScavTrap st2("Ben");
ScavTrap st3;
std::cout << std::endl;
st1.meleeAttack("bob");
st1.rangedAttack("Alf");
std::cout << std::endl;
st2.takeDamage(45);
st2.beRepaired(21);
std::cout << std::endl;
st3.challengeNewcomer();
st3.challengeNewcomer();
std::cout << std::endl;
return (0);
}
int main(int argc, char *argv[])
{
{
std::string s = "a b\"MID\" c d";
std::vector<std::string> result;
unsigned int ret = stringTokenize(s, ' ', &result);
assert(ret == 4);
assert(result.size() == 4);
assert(result[0] == "a");
assert(result[1] == "b\"MID\"");
assert(result[2] == "c");
assert(result[3] == "d");
ret = stringTokenize(s, "\" ", &result);
assert(result.size() == 6);
assert(result[0] == "a");
assert(result[1] == "b");
assert(result[2] == "MID");
assert(result[3] == "");
assert(result[4] == "c");
assert(result[5] == "d");
s = "";
ret = stringTokenize(s, " ", &result);
assert(result.size() == 1);
assert(result[0] == "");
}
{
std::string s = "a b\"MID\" c d";
std::string piece;
std::vector <std::string> result;
StringTokenizer st1(s, ' ');
while (st1.next(&piece)) {
//printf("piece = %s\n", piece.c_str());
result.push_back(piece);
}
assert(result.size() == 4);
assert(result[0] == "a");
assert(result[1] == "b\"MID\"");
assert(result[2] == "c");
assert(result[3] == "d");
result.clear();
StringTokenizer st2(s, "\" ");
while (st2.next(&piece)) {
printf("piece = %s\n", piece.c_str());
result.push_back(piece);
}
assert(result.size() == 6);
assert(result[0] == "a");
assert(result[1] == "b");
assert(result[2] == "MID");
assert(result[3] == "");
assert(result[4] == "c");
assert(result[5] == "d");
result.clear();
s = "";
StringTokenizer st3(s, " ");
while (st3.next(&piece)) {
result.push_back(piece);
}
assert(result.size() == 1);
assert(result[0] == "");
}
{
std::string s = "";
std::string res = stringStrip(s);
assert(res.size() == 0);
s = " ";
res = stringStrip(s);
assert(res.size() == 0);
}
return 0;
}
int main()
{
//Calka z sinusa
cout << "CALKA Z SINUSA" << endl;
double result = 0.0;
TworzenieWatkow calka(0, M_PI, &result);
boost::thread thread(calka);
cout << "Hardware concurrency: " << boost::thread::hardware_concurrency
<< endl;
cout << "Thread ID" << thread.get_id() << endl;
thread.join();
cout << "result" << result << endl;
cout << "DONE!";
getchar();
//-------------------------------------
//Synchronizacja
cout << "SYNCHRONIZACJA" << endl;
mutex characterMutex;
string lancuch;
lancuch.resize(CHARACTERS_TO_WRITE);
thread_group threads;
for (unsigned int i = 0; i < NUMBER_OF_THREADS; ++i)
threads.create_thread(Watek('a'+i,lancuch,characterMutex));
threads.join_all();
cout << lancuch << endl;
cout << "DONE!";
getchar();
//----------------------------------------
//Zmienne warunkowe
cout << "ZMIENNE WARUNKOWE"<<endl;
mutex dataMutex;
Monitor<char>container(dataMutex);
thread_group conditional;
mutex consoleMutex;
for (int i = 0; i < 5; i++) {
conditional.create_thread(Consumer(container,i,consoleMutex));
conditional.create_thread(Producer(container,i,consoleMutex));
}
conditional.join_all();
cout << "DONE!";
getchar();
//------------------------------------
//Pociagi/semafory
cout << "STACJA KOLEJOWA"<<endl;
Peron p1("p1"), p2("p2"), p3("p3");
Train tr1 = Train("T1", p2, p1);
boost::thread t1(tr1);
boost::thread t2(Train("T2", p2, p3));
boost::thread t3(Train("T3", p2, p1));
boost::thread t4(Train("T4", p2, p3));
t1.join();
t2.join();
t3.join();
t4.join();
cout << "DONE"<<endl;
getchar();
cout << "FILOZOFOWIE" << endl;
Semafor eating(PHILOSOPHERS - 1);
Fork* forks[5];
thread_group philosophers;
for (int i = 0; i<PHILOSOPHERS; i++)
{
forks[i] = new Fork(i);
}
for (int i = 0; i<PHILOSOPHERS; i++)
{
philosophers.create_thread(Philosopher(i, forks[i], forks[(i + (PHILOSOPHERS -1)) % PHILOSOPHERS], eating));
}
philosophers.join_all();
cout << "DONE"<<endl;
getchar();
cout << "TASK 1" << endl;
mutex tConsoleMutex;
Task1 taskOne(tConsoleMutex,0);
Task1 taskTwo(tConsoleMutex,1);
boost::thread th1(taskOne);
boost::thread th2(taskTwo);
th1.join();
th2.join();
cout << "DONE" << endl;
getchar();
cout << "TASK 2" << endl;
boost::mutex task2Mutex;
Task2 task2DataGenerator(100);
boost::thread task2Thread(task2DataGenerator);
boost::unique_lock<mutex>task2Lock(task2Mutex);
task2DataGenerator.task2isGeneratingData->wait(task2Lock);
for (int i = 0; i < 100; i++)cout << task2Array[i] << endl;
cout << "DONE" << endl;
getchar();
cout << "TASK 3" << endl;
thread_group task3Group;
Semafor task3Semafor(1);
Semafor task3Max3ThreadsSemafor(3);
for (int i = 0; i < 10; i++) {
task3Group.create_thread(Task3(task3Max3ThreadsSemafor,task3Semafor,i));
}
task3Group.join_all();
cout << "DONE" << endl;
getchar();
cout << "SMOLKA EXAM"<<endl;
cout << "TASK 1"<<endl;
boost::mutex sConsoleMutex;
STask1 st1(sConsoleMutex);
STask1 st2(sConsoleMutex);
boost::thread sTask1Thread(st1);
boost::thread sTask1Thread2(st2);
sTask1Thread.join();
sTask1Thread2.join();
cout << "DONE" << endl;
getchar();
cout << "TASK 2" << endl;
sN = 75;
boost::thread sTask2Thread(sTask2);
boost::mutex sTask2Mutex;
boost::unique_lock<mutex>sTask2Lock(sTask2Mutex);
sTask2Condition.wait(sTask2Lock);
for (int i = 0; i < 75; i++) {
cout<< sTask2Array[i]<<endl;
}
getchar();
return 0;
}
void stratifysites::run () {
cout << "# Parameters\n";
cout << "# thresh1=" << thresh1 << "\n";
cout << "# thresh2=" <<thresh2 << "\n";
cout << "# tlength="<<tlength << "h\n";
cout << "# genpos="<<usegenpos << "\n";
cout << "# strict="<<strict << "\n";
cout << "# bin="<<bins << "\n";
cout << "# predfile="<<predfile << "\n";
cout << "# snpfile="<<snpfile << "\n";
cout << "# genofile="<<genofile << "\n";
cout << "## SNP id\n";
cout << "## Chromosome \n";
cout << "## Genetic position\n";
cout << "## Physical position\n";
cout << "## Average posterior probability of N on derived alleles \n";
cout << "## Average posterior probability of N on ancestral alleles \n";
cout << "## Number of derived alleles that are predicted to be Neandertal \n";
cout << "## Total number of derived alleles \n";
cout << "## Number of ancestral alleles that are predicted to be Neandertal \n";
cout << "## Total number of ancestral alleles \n";
if (givenprefix) {
cout.setf(ios::fixed,ios::floatfield);
cout.precision(3);
}
for (int c = 0 ; c < nchr; c++) {
vector<snp> snps = geno->snps[geno->chrs[c]];
vector<int> tmppred (nind, 0);
vector<double> reg (nind,0);
vector<double> reg2 (nind,0);
vector<double> st1 (nind,0);
vector<double> st2 (nind,0);
vector<int> startpos (nind, 0);
vector<double> maxlengths(snps.size(), 0 );
vector<double> avglengths(snps.size(), 0 );
vector<double> maxglengths(snps.size(), 0 );
vector<double> avgglengths(snps.size(), 0 );
vector<int> denomlengths(snps.size(), 0 );
unordered_map <string, double> plmap ;
unordered_map <string, double> glmap ;
int incontig = 0 ;
int contigsnps = 0;
string contigchr;
double contigstart = 0;
double contigend = 0 ;
double contigl = 0 ;
double contigavganc = 0;
double avgpredanc = 0;
for (int i = 0 ; i < snps.size() ; i++) {
for (int j = 0 ; j < nind; j++) {
double p = (*predanc).get(c,i,j);
tmppred [j] = (p>thresh1)?1:0;
avgpredanc += p;
}
string id = snps[i].id;
string chr = snps[i].chr;
if (nind>0)
avgpredanc /= nind ;
if (i==0) {
for (int j = 0 ; j < nind ; j++) {
reg[j] =reg2[j] = 0;
st1[j] = st2[j] = tmppred[j];
startpos[j] = 0;
}
} else {
int count1 = 0 ;
int count2 = 0;
for (int j = 0 ; j < nind; j++) {
int flag1 = 0;
int flag2 = 0;
int len1 = 0 ;
double len2 = 0;
double avgconf = 0 ;
double trueconf = 0 ;
int denom = 0 ;
int start = 0 ;
int end = 0 ;
if (st1[j] == 0 && tmppred[j] > 0) {
st1[j] = 1;
startpos[j] = i;
} else if (st1[j]==1 && tmppred[j]==0) {
len1 = reg[j];
for (int k = i - 1; k >= 0 && k >= startpos[j] ; k--) {
if ( maxlengths[k] < len1) {
maxlengths[k] = len1;
}
avglengths[k] += len1;
denomlengths[k]++;
start = snps[k].physpos;
avgconf += (*predanc).get (c,k,j);
if (giventrue)
trueconf += (*trueanc)(c,k,j);
denom ++;
string key = chr + ":" + tostring(k) +":"+ tostring(j);
plmap[key] = len1;
}
avgconf = (denom>0)?avgconf/denom:0;
trueconf = (denom>0)?trueconf/denom:0;
reg[j] = 0;
st1[j] = 0;
flag1 = 1;
end = snps[i-1].physpos;
if (len1 > 0) count1++;
} else if (st1[j]==1 && tmppred[j] > 0 ) {
reg[j] += tmppred[j] *(snps[i].physpos - snps[i-1].physpos);
count2 ++;
} else {
}
if (st2[j] == 0 && tmppred[j] > 0)
st2[j] = 1;
else if (st2[j]==1 && tmppred[j]==0) {
len2 = reg2[j];
for (int k = i - 1; k >= 0 && k >= startpos[j] ; k--) {
if (maxglengths[k] < len2) {
maxglengths[k] = len2;
}
avgglengths[k] += len2;
string key = chr + ":" + tostring(k) +":"+ tostring(j);
glmap[key] = len2;
}
reg2[j] = 0;
st2[j] = 0 ;
flag2 = 1;
} else if (st2[j]==1 && tmppred[j] > 0 ) {
reg2[j] += tmppred[j] *(snps[i].genpos - snps[i-1].genpos);
} else {
}
if (flag1 && flag2) {
if (givenprefix) {
len2 *= 100;
}
}
}
if (count2 > 0 ) {
if (incontig) {
contigsnps ++;
contigavganc += avgpredanc;
} else {
contigchr = geno->chrs[c];
contigstart = snps[i-1].physpos;
incontig = 1;
}
contigl += (snps[i].physpos - snps[i-1].physpos);
} else if (count2 == 0 && count1 > 0) {
contigend = snps[i].physpos;
if (contigsnps > 0)
contigavganc /= contigsnps;
long cs = contigstart;
long ce = contigend;
contigl = 0 ;
incontig = 0 ;
contigsnps = 0 ;
contigavganc = 0 ;
}
}
}
for (int i = 0 ; i < snps.size() ; i++) {
string id = snps[i].id;
string chr = snps[i].chr;
double pos = snps[i].physpos;
double gpos = snps[i].genpos;
int n1 = 0;
int n2 = 0;
double n3 = 0;
double n3a = 0 ;
double n4 = 0;
double g = 0 ;
double f = 0 ;
double f2 = 0 ;
int denom2 = 0 ;
double f1 = 0 ;
int denom1 = 0 ;
int d = 0 ;
int a = 0 ;
int dn = 0 ;
int an = 0;
double maxl = 0 ;
double maxgl = 0;
for (int j = 0 ; j < nind ; j++) {
string key = chr + ":" + tostring(i) + ":" + tostring(j);
double panc = (*predanc).get(c,i,j);
if (io::debug >= 1)
cout << "panc ( " << c <<","<<i<<","<<j<<") = " << panc << endl;
int predn = 0 ;
int predh = 0 ;
double predl = 0 ;
if (usegenpos) {
if ( glmap.find(key) != glmap.end())
predl = glmap[key] * 100;
if (maxgl < predl)
maxgl = predl;
} else {
if ( plmap.find(key) != plmap.end())
predl = plmap[key];
if (maxl < predl)
maxl = predl;
}
if ( panc >= thresh1 && predl >= tlength)
predn = 1;
if (panc <= thresh2)
predh = 1;
int allele = (*geno)(c,i,j);
f += allele;
if (allele==1) {
d ++;
n1 += predn;
n2 += predh;
n3 += panc;
if (predn )
dn ++;
}
if (allele==0) {
n3a += panc;
a ++;
if (predn )
an ++;
}
n4 += panc;
if (predn) {
f1 += allele;
denom1++;
}
if (predh) {
f2 += allele;
denom2 ++;
}
}
f /= nind;
g /= nind;
f1 = denom1>0?(f1/denom1):0;
f2 = denom2>0?(f2/denom2):0;
if (d>0) {
n1/=d; n2/=d; n3/=d;
}
if (a>0) {
n3a /= a;
}
if (nind > 0)
n4 /= nind;
int m1 = (n1>=1)?1:0;
int m2 = ( (n1>0)&&(n2>0))?1:0;
cout << id << "\t" << chr << "\t" << gpos*100 << "\t" << snps[i].getphyspos ();
cout << "\t" << n3 << "\t" << n3a ;
cout << "\t" << dn << "\t" << d << "\t" << an << "\t" << a;
cout << endl;
if (denomlengths[i]>0) {
avglengths[i] /= denomlengths[i];
avgglengths[i] /= denomlengths[i];
}
if (givenprefix) {
maxglengths[i] *= 100;
avgglengths[i] *= 100;
long ml = maxlengths[i];
long al = avglengths[i];
}
}
}
}
US_USE_NAMESPACE
int usServiceTrackerTest(int /*argc*/, char* /*argv*/[])
{
US_TEST_BEGIN("ServiceTrackerTest")
ModuleContext* mc = GetModuleContext();
SharedLibraryHandle libS("TestModuleS");
// Start the test target to get a service published.
try
{
libS.Load();
}
catch (const std::exception& e)
{
US_TEST_FAILED_MSG( << "Failed to load module, got exception: " << e.what() );
}
// 1. Create a ServiceTracker with ServiceTrackerCustomizer == null
std::string s1("org.cppmicroservices.TestModuleSService");
ServiceReference servref = mc->GetServiceReference(s1 + "0");
US_TEST_CONDITION_REQUIRED(servref != 0, "Test if registered service of id org.cppmicroservices.TestModuleSService0");
ServiceControlInterface* serviceController = mc->GetService<ServiceControlInterface>(servref);
US_TEST_CONDITION_REQUIRED(serviceController != 0, "Test valid service controller");
std::auto_ptr<ServiceTracker<> > st1(new ServiceTracker<>(mc, servref));
// 2. Check the size method with an unopened service tracker
US_TEST_CONDITION_REQUIRED(st1->Size() == 0, "Test if size == 0");
// 3. Open the service tracker and see what it finds,
// expect to find one instance of the implementation,
// "org.cppmicroservices.TestModuleSService0"
st1->Open();
std::string expName = "TestModuleS";
std::list<ServiceReference> sa2;
st1->GetServiceReferences(sa2);
US_TEST_CONDITION_REQUIRED(sa2.size() == 1, "Checking ServiceTracker size");
std::string name(us_service_impl_name(mc->GetService(sa2.front())));
US_TEST_CONDITION_REQUIRED(name == expName, "Checking service implementation name");
// 5. Close this service tracker
st1->Close();
// 6. Check the size method, now when the servicetracker is closed
US_TEST_CONDITION_REQUIRED(st1->Size() == 0, "Checking ServiceTracker size");
// 7. Check if we still track anything , we should get null
sa2.clear();
st1->GetServiceReferences(sa2);
US_TEST_CONDITION_REQUIRED(sa2.empty(), "Checking ServiceTracker size");
// 8. A new Servicetracker, this time with a filter for the object
std::string fs = std::string("(") + ServiceConstants::OBJECTCLASS() + "=" + s1 + "*" + ")";
LDAPFilter f1(fs);
st1.reset(new ServiceTracker<>(mc, f1));
// add a service
serviceController->ServiceControl(1, "register", 7);
// 9. Open the service tracker and see what it finds,
// expect to find two instances of references to
// "org.cppmicroservices.TestModuleSService*"
// i.e. they refer to the same piece of code
st1->Open();
sa2.clear();
st1->GetServiceReferences(sa2);
US_TEST_CONDITION_REQUIRED(sa2.size() == 2, "Checking service reference count");
for (std::list<ServiceReference>::const_iterator i = sa2.begin(); i != sa2.end(); ++i)
{
std::string name(mc->GetService(*i)->GetNameOfClass());
US_TEST_CONDITION_REQUIRED(name == expName, "Check for expected class name");
}
// 10. Get libTestModuleS to register one more service and see if it appears
serviceController->ServiceControl(2, "register", 1);
sa2.clear();
st1->GetServiceReferences(sa2);
US_TEST_CONDITION_REQUIRED(sa2.size() == 3, "Checking service reference count");
for (std::list<ServiceReference>::const_iterator i = sa2.begin(); i != sa2.end(); ++i)
{
std::string name(mc->GetService(*i)->GetNameOfClass());
US_TEST_CONDITION_REQUIRED(name == expName, "Check for expected class name");
}
// 11. Get libTestModuleS to register one more service and see if it appears
serviceController->ServiceControl(3, "register", 2);
sa2.clear();
st1->GetServiceReferences(sa2);
US_TEST_CONDITION_REQUIRED(sa2.size() == 4, "Checking service reference count");
for (std::list<ServiceReference>::const_iterator i = sa2.begin(); i != sa2.end(); ++i)
{
std::string name = mc->GetService(*i)->GetNameOfClass();
US_TEST_CONDITION_REQUIRED(name == expName, "Check for expected class name");
}
// 12. Get libTestModuleS to unregister one service and see if it disappears
serviceController->ServiceControl(3, "unregister", 0);
sa2.clear();
st1->GetServiceReferences(sa2);
US_TEST_CONDITION_REQUIRED(sa2.size() == 3, "Checking service reference count");
for (std::list<ServiceReference>::const_iterator i = sa2.begin(); i != sa2.end(); ++i)
{
std::string name = mc->GetService(*i)->GetNameOfClass();
US_TEST_CONDITION_REQUIRED(name == expName, "Check for expected class name");
}
// 13. Get the highest ranking service reference, it should have ranking 7
ServiceReference h1 = st1->GetServiceReference();
int rank = any_cast<int>(h1.GetProperty(ServiceConstants::SERVICE_RANKING()));
US_TEST_CONDITION_REQUIRED(rank == 7, "Check service rank");
// 14. Get the service of the highest ranked service reference
US_BASECLASS_NAME* o1 = st1->GetService(h1);
US_TEST_CONDITION_REQUIRED(o1 != 0, "Check for non-null service");
// 14a Get the highest ranked service, directly this time
US_BASECLASS_NAME* o3 = st1->GetService();
US_TEST_CONDITION_REQUIRED(o3 != 0, "Check for non-null service");
US_TEST_CONDITION_REQUIRED(o1 == o3, "Check for equal service instances");
// 15. Now release the tracking of that service and then try to get it
// from the servicetracker, which should yield a null object
serviceController->ServiceControl(1, "unregister", 7);
US_BASECLASS_NAME* o2 = st1->GetService(h1);
US_TEST_CONDITION_REQUIRED(o2 == 0, "Checkt that service is null");
// 16. Get all service objects this tracker tracks, it should be 2
std::list<US_BASECLASS_NAME*> ts1;
st1->GetServices(ts1);
US_TEST_CONDITION_REQUIRED(ts1.size() == 2, "Check service count");
// 17. Test the remove method.
// First register another service, then remove it being tracked
serviceController->ServiceControl(1, "register", 7);
h1 = st1->GetServiceReference();
std::list<ServiceReference> sa3;
st1->GetServiceReferences(sa3);
US_TEST_CONDITION_REQUIRED(sa3.size() == 3, "Check service reference count");
for (std::list<ServiceReference>::const_iterator i = sa3.begin(); i != sa3.end(); ++i)
{
std::string name = mc->GetService(*i)->GetNameOfClass();
US_TEST_CONDITION_REQUIRED(name == expName, "Checking for expected class name");
}
st1->Remove(h1); // remove tracking on one servref
sa2.clear();
st1->GetServiceReferences(sa2);
US_TEST_CONDITION_REQUIRED(sa2.size() == 2, "Check service reference count");
// 18. Test the addingService method,add a service reference
// 19. Test the removedService method, remove a service reference
// 20. Test the waitForService method
US_BASECLASS_NAME* o9 = st1->WaitForService(50);
US_TEST_CONDITION_REQUIRED(o9 != 0, "Checking WaitForService method");
US_TEST_END()
}
double simulate_with_dependence (string treeFile, double PI_1, double init_k, int total_positions, int num_pos_with_same_k, double k_increase, int is_gamma, double alpha, double beta, int num_cat)
{
//read Newick format tree
tree treeIn(treeFile);
//four states alphabet A C G T (will later be rplaced to 00,01,10,11)
alphabet* alph = new nucleotide;
sequenceContainer SC_all; //this will contain all positions
//parameters:
double PI_0 = 1-PI_1;
double k = init_k; //will be increased with each iteration
//parameters:
int jump_size = total_positions / num_pos_with_same_k;
for(int i=0; i<jump_size; i++)
{
Vdouble freqs; //stationary probabilities PI_00, PI_01, PI_10, PI_11
double TOTAL = k*PI_1*PI_1 + 2*PI_0*PI_1 + k*PI_0*PI_0;
freqs.push_back(k*PI_0*PI_0 / TOTAL); //PI_00 = k*PI_0*PI_0 / TOTAL
freqs.push_back(PI_0*PI_1 / TOTAL); //PI_01 = PI_0*PI_1 / TOTAL
freqs.push_back(PI_0*PI_1 / TOTAL); //PI_10 = PI_0*PI_1 / TOTAL
freqs.push_back(k*PI_1*PI_1 / TOTAL); //PI_11 = k*PI_1*PI_1 / TOTAL
//Q matrix (partial values - the rest are calculated by gtrModel using freqs and these values)
MDOUBLE a2c = PI_1; // --> c2a = freqs[a]*a2c/freqs[c] --> c2a = ((k*PI_0*PI_0 / TOTAL)*PI_1)/(PI_0*PI_1 / TOTAL) = k*PI_0
MDOUBLE a2g = PI_1;
MDOUBLE a2t = 0;
MDOUBLE c2g = 0;
MDOUBLE c2t = k*PI_1;
MDOUBLE g2t = k*PI_1;
//starting the evolutionary model
distribution *currDist = NULL;
if(is_gamma == 1)
{
currDist = new generalGammaDistribution(alpha,beta,num_cat); // ---> in the future we might want to turn these into param
}
else
{
currDist = new uniDistribution; // no among site rate variation
}
replacementModel *probMod = NULL;
pijAccelerator *pijAcc = NULL;
probMod = new gtrModel(freqs,a2c,a2g,a2t,c2g,c2t,g2t);
pijAcc = new trivialAccelerator(probMod);
stochasticProcess* _sp = new stochasticProcess(currDist, pijAcc);
//simulate:
simulateTree st1(treeIn, *_sp, alph);
st1.generate_seq(num_pos_with_same_k); //simulate num_pos_with_same_k positions with the current k
if(i == 0)
{
SC_all = st1.toSeqDataWithoutInternalNodes(); //first time
}
else
{
sequenceContainer SC = st1.toSeqDataWithoutInternalNodes(); //concatenate new positions to the ones you have
SC_all.concatenate(SC);
}
delete currDist;
delete probMod;
delete pijAcc;
delete _sp;
k = k + k_increase; //k = 1 , 1.05 , 1.1 , ... , 5.5
}
//prepare out file name:
std::stringstream sstm;
if(is_gamma == 1)
{
sstm << treeFile << ".gammaRateNoInv.PI_1=" << PI_1 << ".init_k=" << init_k << ".k_group_size=" << num_pos_with_same_k << ".k_increase=" << k_increase << ".fas";
}
else
{
sstm << treeFile << ".NoRate.PI_1=" << PI_1 << ".init_k=" << init_k << ".k_group_size=" << num_pos_with_same_k << ".k_increase=" << k_increase << ".fas";
}
std::string seqOutputFile = sstm.str();
//write out:
ofstream seq_sim(seqOutputFile.c_str());
fastaFormat::write(seq_sim,SC_all);
seq_sim.close();
delete alph;
return 0;
}
main ()
{
// CL_StringSequence tst (18000); // Testing big sequences
CL_StringSequence a;
a.Add ("world!");
a.Add ("Hello,");
a.Add ("this is");
a.Add ("a great day.");
PrintOut (a);
a.Insert ("world! 2", 1);
PrintOut (a);
a.Insert ("Hello, 2", -1);
PrintOut (a);
a.Insert ("this is 2", 2);
PrintOut (a);
a.Insert ("a great day. 2", 3);
PrintOut (a);
a.Sort();
PrintOut (a);
#ifndef __GNUC__ // GCC Still has bugs!
CL_IntegerSet st1(2,4);
st1.Add (4);
st1.Add (7);
st1.Add (8);
st1.Add (9);
CL_StringSequence sq = a - st1;
PrintOut (sq);
#endif
a.ShiftRightAt (2);
PrintOut (a);
a[2] = "Some string here";
PrintOut (a);
a.ShiftLeftAt (2, 2);
PrintOut (a);
CL_StringSequence* b = new CL_StringSequence(10);
*b = a;
PrintOut (*b);
*b += a;
PrintOut (*b);
b->Sort();
PrintOut (*b);
CL_BinaryFile f ("seqtest.dat", TRUE);
f << *b; // Testing persistent sequences
b->MakeEmpty ();
// CL_Builder<CL_String> aBuilder;
// CL_ObjectSequence a2(0, &aBuilder);
CL_ObjectSequence a2;
CL_String* pStrg;
pStrg = new CL_String ("1"); a2.Add (pStrg);
pStrg = new CL_String ("2"); a2.Add (pStrg);
pStrg = new CL_String ("3"); a2.Add (pStrg);
pStrg = new CL_String ("10"); a2.Add (pStrg);
pStrg = new CL_String ("20"); a2.Add (pStrg);
pStrg = new CL_String ("30"); a2.Add (pStrg);
pStrg = new CL_String ("11"); a2.Add (pStrg);
pStrg = new CL_String ("22"); a2.Add (pStrg);
pStrg = new CL_String ("31"); a2.Add (pStrg);
pStrg = new CL_String ("10"); a2.Add (pStrg);
printf ("a2's size: %ld\n", a2.Size());
f << a2; // Testing persistent sequences
f.SeekToBegin();
f >> *b;
// b->ReadFrom (f);
printf ("Restored b is: \n"); PrintOut (*b);
delete b;
long i;
for (i = 0; i < a2.Size(); i++) {
printf ("'%s'\n", ((CL_String*) a2[i])->AsPtr());
}
pStrg = (CL_String*) a2.ExtractLeftmost();
printf ("Leftmost: '%s'\n", pStrg->AsPtr());
for (i = 0; i < a2.Size(); i++) {
printf ("'%s'\n", ((CL_String*) a2[i])->AsPtr());
}
delete pStrg;
pStrg = (CL_String*) a2[4];
a2.Remove (4);
delete pStrg;
for (i = 0; i < a2.Size(); i++) {
printf ("'%s'\n", ((CL_String*) a2[i])->AsPtr());
}
a2.DestroyContents ();
f >> a2;
printf ("Restored a2 is:\n");
for (i = 0; i < a2.Size(); i++) {
printf ("'%s'\n", ((CL_String*) a2[i])->AsPtr());
}
printf ("------------------------------------\n");
a2.DestroyContents ();
CL_IntegerSequence iseq;
for (i = 0; i < 100; i++) {
iseq.Add (i);
iseq.Add (5*i);
}
for (i = 5; i < 80; i++)
iseq.Remove (2);
iseq.Add (253);
printf ("iseq size %ld\n", iseq.Size());
long j;
for (j = 0; j < iseq.Size(); j++) {
printf ("iseq[%ld] = %ld\n", j, iseq[j]);
}
iseq.Sort();
printf ("==============================\niseq size %ld\n", iseq.Size());
for (j = 0; j < iseq.Size(); j++) {
printf ("iseq[%ld] = %ld\n", j, iseq[j]);
}
iseq.Sort();
return 0;
}