/*
Merges two VectorSiteContainers into a single VectorSiteContainer
*/
shared_ptr<VectorSiteContainer> merge_vscs(shared_ptr<VectorSiteContainer> s1, shared_ptr<VectorSiteContainer> s2)
throw (AlphabetMismatchException, Exception)
{
if (s1->getAlphabet()->getAlphabetType() != s2->getAlphabet()->getAlphabetType())
throw AlphabetMismatchException("SiteContainerTools::merge.", s1->getAlphabet(), s2->getAlphabet());
auto alphabet = s1->getAlphabet();
const int unknown_char = alphabet->getUnknownCharacterCode();
size_t l1 = s1->getNumberOfSites();
size_t l2 = s2->getNumberOfSites();
auto n1 = s1->getSequencesNames();
auto n2 = s2->getSequencesNames();
vector<string> allnames = merge_vectors(n1, n2);
unique_ptr<VectorSequenceContainer> tmp_container(new VectorSequenceContainer(alphabet));
for (auto &n : allnames) {
vector<int> seqvec1;
vector<int> seqvec2;
seqvec1.reserve(l1+l2);
seqvec2.reserve(l2);
if (s1->hasSequence(n)) {
auto tmpvec = s1->getSequence(n).getContent();
seqvec1.insert( seqvec1.end(), tmpvec.begin(), tmpvec.end());
}
else {
vector<int> tmpvec(l1, unknown_char);
seqvec1.insert( seqvec1.end(), tmpvec.begin(), tmpvec.end());
}
if (s2->hasSequence(n)) {
auto tmpvec = s2->getSequence(n).getContent();
seqvec2.insert( seqvec2.end(), tmpvec.begin(), tmpvec.end());
}
else {
vector<int> tmpvec(l2, unknown_char);
seqvec2.insert( seqvec2.end(), tmpvec.begin(), tmpvec.end());
}
seqvec1.insert(seqvec1.end(), seqvec2.begin(), seqvec2.end());
unique_ptr<BasicSequence> seq(new BasicSequence(n, seqvec1, alphabet));
tmp_container->addSequence(*seq, false);
}
auto output = make_shared<VectorSiteContainer>(*tmp_container);
return output;
}
std::vector<int> Lotto(int qty, int ch)
{
int buff[qty];
for (int i = 1, limit = qty+1; i < limit; i++ )
buff[i-1] = i;
std::vector<int> tmpvec (buff, buff + qty);
std::vector<int> tmpres(ch);
std::random_shuffle(tmpvec.begin(), tmpvec.end());
std::copy(tmpvec.begin(), tmpvec.begin()+ch, tmpres.begin());
return tmpres;
}
void egHWU::rdWeight(string inputfile)
{
gfun::printLOG("Reading Weight Matrix at [ " + inputfile + " ]\n");
ifstream result(inputfile.c_str());
if(!result) gfun::error("\ncould not read the Weight Matrix file\n");
//result<<"#result of association scanning (0=A1A1, 1=A1A2, 2=A2A2)\n";
//result<<"#order\t"<<"Chr\tName\tPos\tBp\tAllel1\tAllel2\t"<<"P_value\n";
//vector<string> str_vec;
//string buf_str;
//getline(result,buf_str);
//int dim=gfun::split_string(buf_str,str_vec);
int dim=0;
result>>dim;
if(dim!=_n_sub) gfun::error("Dim of Matrix != sample size\n");
vector<double> tmpvec(dim,0);
vector< vector<double> > weight(dim,tmpvec);
double tmp;
for(int i=0; i<_n_sub; i++){
for(int j=i; j<_n_sub; j++){
result>>tmp;
double tmptmp=tmp;
weight[i][j]=tmptmp;
weight[j][i]=weight[i][j];
//_weight->assign(i,j,tmp);
//_weight->assign(j,i,tmp);
}
}
result.close();
//assign to _weight
_Kappa.resize(_n_sub,_n_sub);
for(int i=0; i<weight.size(); i++){
for(int j=0; j<_n_sub; j++){
_Kappa(i,j)=weight[i][j];
}
}
_weight_flag=true;
cout<<"\nRelateness Matrix Done.\n\n";
}
unsigned int optCoef(arma::mat& weights, const arma::icube& obs, const arma::cube& emission,
const arma::mat& initk, const arma::cube& beta, const arma::mat& scales, arma::mat& coef,
const arma::mat& X, const arma::ivec& cumsumstate, const arma::ivec& numberOfStates,
int trace) {
int iter = 0;
double change = 1.0;
while ((change > 1e-10) & (iter < 100)) {
arma::vec tmpvec(X.n_cols * (weights.n_rows - 1));
bool solve_ok = arma::solve(tmpvec, hCoef(weights, X),
gCoef(obs, beta, scales, emission, initk, weights, X, cumsumstate, numberOfStates));
if (solve_ok == false) {
return (4);
}
arma::mat coefnew(coef.n_rows, coef.n_cols - 1);
for (unsigned int i = 0; i < (weights.n_rows - 1); i++) {
coefnew.col(i) = coef.col(i + 1) - tmpvec.subvec(i * X.n_cols, (i + 1) * X.n_cols - 1);
}
change = arma::accu(arma::abs(coef.submat(0, 1, coef.n_rows - 1, coef.n_cols - 1) - coefnew))
/ coefnew.n_elem;
coef.submat(0, 1, coef.n_rows - 1, coef.n_cols - 1) = coefnew;
iter++;
if (trace == 3) {
Rcout << "coefficient optimization iter: " << iter;
Rcout << " new coefficients: " << std::endl << coefnew << std::endl;
Rcout << " relative change: " << change << std::endl;
}
weights = exp(X * coef).t();
if (!weights.is_finite()) {
return (5);
}
weights.each_row() /= sum(weights, 0);
}
return (0);
}
bool NetServer::loadFromSavegame( ClientPtr clt, Cockpit *cp )
{
ObjSerial cltserial = getUniqueSerial();
QVector tmpvec( 0, 0, 0 );
bool update = true;
float credits;
vector< string >savedships;
string str( "" );
COUT<<"-> LOADING SAVE FROM NETWORK"<<endl;
cp->savegame->SetStarSystem( string() );
cp->savegame->ParseSaveGame( "", str, "", tmpvec, update, credits, savedships, cltserial, clt->savegame[0], false );
//Generate the system we enter in if needed and add the client in it
if ( savedships.empty() ) {
COUT<<"There are no saved ships... corrupted save file for "<<clt->callsign<<endl;
std::string logoutnetbuf;
addSimpleChar( logoutnetbuf, ACCT_LOGOUT );
addSimpleString( logoutnetbuf, clt->callsign );
addSimpleString( logoutnetbuf, clt->passwd );
//We can't find the unit saved for player -> send a login error
this->logout( clt );
return false;
}
COUT<<"\tcredits = "<<credits<<endl;
COUT<<"\tfaction = "<<cp->savegame->GetPlayerFaction()<<endl;
COUT<<"-> SAVE LOADED"<<endl;
//WARNING : WE DON'T SAVE FACTION NOR FLIGHTGROUP YET
COUT<<"-> UNIT FACTORY WITH XML"<<endl;
//We may have to determine which is the current ship of the player if we handle several ships for one player
string PLAYER_SHIPNAME = savedships[0];
string PLAYER_FACTION_STRING = cp->savegame->GetPlayerFaction();
int saved_faction = FactionUtil::GetFactionIndex( PLAYER_FACTION_STRING );
//vector<vector <string> > path = lookforUnit( savedships[0].c_str(), saved_faction, false);
bool exist = true; //(VSFileSystem::LookForFile( savedships[0], VSFileSystem::UnitFile)<=VSFileSystem::Ok);
static std::string loadfailed( "LOAD_FAILED" );
Unit *un = NULL;
if ( !PLAYER_SHIPNAME.empty() ) {
un = UnitFactory::createUnit( PLAYER_SHIPNAME.c_str(),
false,
saved_faction,
string( "" ),
Flightgroup::newFlightgroup( clt->callsign, PLAYER_SHIPNAME, PLAYER_FACTION_STRING,
"default", 1, 1, "", "", mission ),
0, &clt->savegame[1] );
}
if (!un) {
exist = false;
} else if (un->name == loadfailed) {
exist = false;
un->Kill();
}
if (!exist) {
unsigned short serial = cltserial;
std::string logoutnetbuf;
addSimpleChar( logoutnetbuf, ACCT_LOGOUT );
addSimpleString( logoutnetbuf, clt->callsign );
addSimpleString( logoutnetbuf, clt->passwd );
//We can't find the unit saved for player -> send a login error
this->logout( clt );
Packet p2;
//Send the account server a logout info
if ( !acct_sock->sendstr( logoutnetbuf ) )
COUT<<"ERROR sending LOGOUT to account server"<<endl;
cerr<<"WARNING : Unit file ("<<savedships[0]<<") not found for "<<clt->callsign<<endl;
return cp;
}
COUT<<"\tAFTER UNIT FACTORY WITH XML"<<endl;
clt->game_unit.SetUnit( un );
//Assign its serial to client*
un->SetSerial( cltserial );
un->SetPosAndCumPos( cp->savegame->GetPlayerLocation() );
//Affect the created unit to the cockpit
COUT<<"-> UNIT LOADED"<<endl;
cp->SetParent( un, PLAYER_SHIPNAME.c_str(), "", tmpvec );
COUT<<"-> COCKPIT AFFECTED TO UNIT"<<endl;
COUT<<"SHIP -- "<<savedships[0]<<" -- LOCATION: x="<<tmpvec.i<<",y="<<tmpvec.j<<",z="<<tmpvec.k<<endl;
return true;
}
bool NetServer::loadFromNewGame( ClientPtr clt, Cockpit *cp, string fighter )
{
ObjSerial cltserial = getUniqueSerial();
string PLAYER_SHIPNAME = fighter;
Mission *mission = NULL;
if (active_missions.size() > 0)
mission = active_missions[0];
if (!mission) {
COUT<<"Cannot login player without acctserver: No missions available";
sendLoginError( clt );
return false;
}
int saved_faction = 0; //NETFIXME: Send faction over network too!
cp->savegame->SetSavedCredits( XMLSupport::parse_float( mission->getVariable( "credits", "0" ) ) );
cp->savegame->SetStarSystem( mission->getVariable( "system", "Sol/Sol" ) );
if ( !mission->flightgroups.empty() )
cp->savegame->SetPlayerFaction( mission->flightgroups[0]->faction );
COUT<<"\tcredits = "<<cp->savegame->GetSavedCredits()<<endl;
COUT<<"\tfaction = "<<cp->savegame->GetPlayerFaction()<<endl;
COUT<<"-> SAVE LOADED"<<endl;
cp->credits = cp->savegame->GetSavedCredits();
//WARNING : WE DON'T SAVE FACTION NOR FLIGHTGROUP YET
COUT<<"-> UNIT FACTORY WITH XML"<<endl;
//We may have to determine which is the current ship of the player if we handle several ships for one player
string PLAYER_FACTION_STRING = cp->savegame->GetPlayerFaction();
saved_faction = FactionUtil::GetFactionIndex( PLAYER_FACTION_STRING );
bool exist = true; //(VSFileSystem::LookForFile( savedships[0], VSFileSystem::UnitFile)<=VSFileSystem::Ok);
static std::string loadfailed( "LOAD_FAILED" );
Unit *un = NULL;
if ( !PLAYER_SHIPNAME.empty() ) {
un = UnitFactory::createUnit( PLAYER_SHIPNAME.c_str(),
false,
saved_faction,
string( "" ),
Flightgroup::newFlightgroup( clt->callsign, PLAYER_SHIPNAME, PLAYER_FACTION_STRING,
"default", 1, 1, "", "", mission ),
0 );
}
if (!un) {
exist = false;
} else if (un->name == loadfailed) {
exist = false;
un->Kill();
}
if (!exist) {
//We can't find the unit saved for player -> send a login error
this->sendLoginError( clt );
cerr<<"WARNING : Unit file ("<<PLAYER_SHIPNAME<<") not found for "<<clt->callsign<<endl;
return false;
}
COUT<<"\tAFTER UNIT FACTORY WITH XML"<<endl;
clt->game_unit.SetUnit( un );
//Assign its serial to client*
un->SetSerial( cltserial );
un->PrimeOrders(); //Accept Comm messages
//Affect the created unit to the cockpit
COUT<<"-> UNIT LOADED"<<endl;
QVector tmpvec( 0, 0, 0 );
cp->SetParent( un, PLAYER_SHIPNAME.c_str(), "", tmpvec );
COUT<<"-> COCKPIT AFFECTED TO UNIT"<<endl;
{
string savestr, xmlstr;
clt->savegame.resize( 0 );
//Get the save parts in a string array
cp->activeStarSystem = zonemgr->addZone( cp->savegame->GetStarSystem() ); //Needed for GetSaveStrings.
SaveNetUtil::GetSaveStrings( clt, savestr, xmlstr, true );
clt->savegame.push_back( savestr );
clt->savegame.push_back( xmlstr );
}
return true;
}
