bool CActiveStormnode::SendStormnodePing(std::string& errorMessage) {
if(status != ACTIVE_STORMNODE_STARTED) {
errorMessage = "Stormnode is not in a running status";
return false;
}
CPubKey pubKeyStormnode;
CKey keyStormnode;
if(!sandStormSigner.SetKey(strStormNodePrivKey, errorMessage, keyStormnode, pubKeyStormnode))
{
errorMessage = strprintf("Error upon calling SetKey: %s\n", errorMessage);
return false;
}
LogPrintf("CActiveStormnode::SendStormnodePing() - Relay Stormnode Ping vin = %s\n", vin.ToString());
CStormnodePing snp(vin);
if(!snp.Sign(keyStormnode, pubKeyStormnode))
{
errorMessage = "Couldn't sign Stormnode Ping";
return false;
}
// Update lastPing for our stormnode in Stormnode list
CStormnode* psn = snodeman.Find(vin);
if(psn != NULL)
{
if(psn->IsPingedWithin(STORMNODE_PING_SECONDS, snp.sigTime)){
errorMessage = "Too early to send Stormnode Ping";
return false;
}
psn->lastPing = snp;
snodeman.mapSeenStormnodePing.insert(make_pair(snp.GetHash(), snp));
//snodeman.mapSeenStormnodeBroadcast.lastPing is probably outdated, so we'll update it
CStormnodeBroadcast snb(*psn);
uint256 hash = snb.GetHash();
if(snodeman.mapSeenStormnodeBroadcast.count(hash)) snodeman.mapSeenStormnodeBroadcast[hash].lastPing = snp;
snp.Relay();
return true;
}
else
{
// Seems like we are trying to send a ping while the Stormnode is not registered in the network
errorMessage = "Sandstorm Stormnode List doesn't include our Stormnode, shutting down Stormnode pinging service! " + vin.ToString();
status = ACTIVE_STORMNODE_NOT_CAPABLE;
notCapableReason = errorMessage;
return false;
}
}
bool CActiveStormnode::Register(CTxIn vin, CService service, CKey keyCollateralAddress, CPubKey pubKeyCollateralAddress, CKey keyStormnode, CPubKey pubKeyStormnode, std::string &errorMessage) {
CStormnodeBroadcast snb;
CStormnodePing snp(vin);
if(!snp.Sign(keyStormnode, pubKeyStormnode)){
errorMessage = strprintf("Failed to sign ping, vin: %s", vin.ToString());
LogPrintf("CActiveStormnode::Register() - %s\n", errorMessage);
return false;
}
snodeman.mapSeenStormnodePing.insert(make_pair(snp.GetHash(), snp));
LogPrintf("CActiveStormnode::Register() - Adding to Stormnode list\n service: %s\n vin: %s\n", service.ToString(), vin.ToString());
snb = CStormnodeBroadcast(service, vin, pubKeyCollateralAddress, pubKeyStormnode, PROTOCOL_VERSION);
snb.lastPing = snp;
if(!snb.Sign(keyCollateralAddress)){
errorMessage = strprintf("Failed to sign broadcast, vin: %s", vin.ToString());
LogPrintf("CActiveStormnode::Register() - %s\n", errorMessage);
return false;
}
snodeman.mapSeenStormnodeBroadcast.insert(make_pair(snb.GetHash(), snb));
stormnodeSync.AddedStormnodeList(snb.GetHash());
CStormnode* psn = snodeman.Find(vin);
if(psn == NULL)
{
CStormnode sn(snb);
snodeman.Add(sn);
} else {
psn->UpdateFromNewBroadcast(snb);
}
//send to all peers
LogPrintf("CActiveStormnode::Register() - RelayElectionEntry vin = %s\n", vin.ToString());
snb.Relay();
return true;
}
void genotype::read_vcf (string genofile, bool isgenoytpe) {
igzstream ig (genofile.c_str());
string line;
vector<snp> tmp;
int j = 0 ;
maxgpos = unordered_map<string, double> ();
mingpos = unordered_map<string, double>();
maxppos = unordered_map<string, double> ();
minppos = unordered_map<string, double>();
chrs = vector<string> ();
double prevgpos ;
double prevppos;
string prevchr="";
int size = 10000;
int inc = 10000;
int linenum = 0 ;
bool setind = false;
int numhap = 2;
if (isgenotype)
numhap = 1;
while (std::getline (ig, line) ) {
linenum ++;
char c = line[0];
if (c=='#') {
if (line.find ("CHROM")!=string::npos) {
if (!givenind) {
vector<string> toks;
functions::tokenize (line.c_str(), toks, " \t");
nind = toks.size() - 9 ;
nind *= numhap;
for (int i = 9 ; i < toks.size(); i++){
string id = toks[i];
indiv.push_back (ind(id,'U',"G"));
if (!isgenotype)
indiv.push_back (ind(id,'U',"G"));
}
setind = true;
}
}
} else {
vector<string> toks;
functions::tokenize (line.c_str(), toks, " \t");
string id = toks[2];
string chr = toks[0];
double physpos = atof(toks[1].c_str());
double genpos = physpos*1.3/1e8;
if (id.compare (".")==0) {
id = chr+":"+toks[1];
}
string ref = toks[3];
string var = toks[4];
string pass = toks[6];
string desc = toks[7];
string format = toks[8];
if (pass.compare("PASS")!=0)
continue;
if (ref.compare (".")==0)
continue;
if (desc.compare (".") == 0 ) {
cout << "Warning: No INFO field found. Assuming site is a SNP " << endl;
}
vector<string> tok1;
functions::tokenize (desc.c_str(), tok1, ";");
if (tok1[0].compare("SNP")!=0)
continue;
// Fill the snps
if (chr.compare(prevchr)==0) {
if (physpos >= prevppos){
prevgpos = genpos;
prevppos = physpos;
} else {
cerr << "Invalid snps in " << genofile <<" : Line " << linenum << "\t Must have non-decreasing physical positions" << endl;
// exit (1);
}
} else {
prevchr = chr;
prevgpos = genpos;
prevppos = physpos;
if (snps.find(chr) != snps.end ()) {
cerr << "Invalid snps in "<< genofile << " : Line " << linenum << "\t SNPs on a chromosome must be consecutive" << endl;
exit (1);
}
chrs.push_back(chr);
snps[chr] = vector<snp>();
// snps[chr].reserve (size);
}
/* if (j==size){
size += inc;
snps[chr].reserve(size);
}
*/
if ( maxppos.find(chr) == maxppos.end()) {
maxppos[chr] = physpos;
} else if (physpos > maxppos[chr])
maxppos[chr] = physpos;
if ( minppos.find(chr) == minppos.end()) {
minppos[chr] = physpos;
} else if (physpos < minppos[chr])
minppos[chr] = physpos;
if ( maxgpos.find(chr) == maxgpos.end()) {
maxgpos[chr] = genpos;
} else if (genpos > maxgpos[chr])
maxgpos[chr] = genpos;
if ( mingpos.find(chr) == mingpos.end()) {
mingpos[chr] = genpos;
} else if (genpos < mingpos[chr])
mingpos[chr] = genpos;
// Fill in the genotypes
tok1.resize (0);
functions::tokenize (format.c_str(), tok1,":");
int gind = -1;
for (int i = 0 ; i < tok1.size(); i++){
if (tok1[i].compare ("GT")==0) {
gind = i;
break;
}
}
if (gind == -1)
continue;
snps[chr].push_back (snp(id,chr,physpos,genpos,var,ref));
vector<int> >ype = snps[chr].back().gtype;
j++;
if (setind) {
if (nind != numhap*(toks.size()-9)){
cerr << "Bad genotype in " << genofile << ": Line "<< linenum << endl;
exit(1);
}
} else {
nind = toks.size() - 9;
nind *= numhap;
setind = true;
}
gtype.resize(nind, 9);
for (int i = 9, k = 0; i < toks.size(); i++, k++){
tok1.resize(0);
functions::tokenize(toks[i], tok1,",");
if (isgenotype) {
int a1 = tok1[gind][0];
int a2 = tok1[gind][2];
gtype[k] = (a1-48) + (a2-48);
} else {
int a1 = tok1[gind][0];
int a2 = tok1[gind][2];
gtype[2*k] = a1-48;
gtype[2*k+1] = a2-48;
}
}
}
if (j%10000==0) {
io::println ("Read " + tostring (j) + " lines" ,0);
}
}
nchr = chrs.size ();
nsnps = j;
if (io::debug >= 2 ) {
cout << "genotype = " << to_string ();
}
ig.close ();
}
void genotype::read_snps (string filename){
ifstream inp (filename.c_str());
if (!inp.is_open()){
cerr << "Error reading file "<< filename <<endl;
exit(1);
}
string line;
vector<snp> tmp;
int j = 0 ;
maxgpos = unordered_map<string, double> ();
mingpos = unordered_map<string, double>();
maxppos = unordered_map<string, double> ();
minppos = unordered_map<string, double>();
chrs = vector<string> ();
double prevgpos ;
double prevppos;
string prevchr="";
int linenum = 0;
while ( std::getline (inp, line)){
linenum ++;
char c = line[0];
if (c=='#')
continue;
istringstream ss (line);
if (line.empty())
continue;
string id;
string chr;
double genpos;
double physpos;
string var;
string ref;
ss >> id;
ss >> chr;
ss >> genpos;
ss >> physpos;
ss >> var;
ss >> ref;
if (chr.compare(prevchr)==0) {
if (physpos >= prevppos){
prevgpos = genpos;
prevppos = physpos;
} else {
cerr << "Invalid snp file " << filename <<" : Line " << linenum << "\t Must have non-decreasing physical positions" << endl;
// exit (1);
}
} else {
prevchr = chr;
prevgpos = genpos;
prevppos = physpos;
if (snps.find(chr) != snps.end ()) {
cerr << "Invalid snp file "<<filename << " : Line " << linenum << "\t SNPs on a chromosome must be consecutive" << endl;
exit (1);
}
chrs.push_back(chr);
snps[chr] = vector<snp>();
}
snps[chr].push_back (snp(id,chr,physpos,genpos,var,ref));
j++;
if ( maxppos.find(chr) == maxppos.end()) {
maxppos[chr] = physpos;
} else if (physpos > maxppos[chr])
maxppos[chr] = physpos;
if ( minppos.find(chr) == minppos.end()) {
minppos[chr] = physpos;
} else if (physpos < minppos[chr])
minppos[chr] = physpos;
if ( maxgpos.find(chr) == maxgpos.end()) {
maxgpos[chr] = genpos;
} else if (genpos > maxgpos[chr])
maxgpos[chr] = genpos;
if ( mingpos.find(chr) == mingpos.end()) {
mingpos[chr] = genpos;
} else if (genpos < mingpos[chr])
mingpos[chr] = genpos;
}
nsnps = j;
nchr = chrs.size();
int cumnum = 0;
cumnumsnps.resize (nchr);
for (int i = 0 ; i < nchr; i++) {
numsnps[chrs[i]] = snps[chrs[i]].size();
cumnumsnps[i] = cumnum;
cumnum += numsnps[chrs[i]];
allsnps.insert ( snps[chrs[i]].begin(),snps[chrs[i]].end());
vector<snp> &tmpsnps = snps[chrs[i]];
for (int j = 0 ; j < tmpsnps.size(); j++){
snp &s= tmpsnps[j];
if (allsnpsmap.find(s.id) != allsnpsmap.end()){
cerr << "Duplicate SNP ids " << s.id <<endl;
exit(1);
}
allsnpsmap[s.id] = pair<string,int>(s.chr,j);
}
}
inp.close();
}
const real iterate(
const int n,
real4 pos[],
real4 vel[],
real4 acc[],
real4 jrk[],
const real eta,
const real eps2,
const real dt)
{
std::vector<real4> acc0(n), jrk0(n);
const real dt2 = dt*(1.0/2.0);
const real dt3 = dt*(1.0/3.0);
for (int i = 0; i < n; i++)
{
acc0[i] = acc[i];
jrk0[i] = jrk[i];
pos[i].x += dt*(vel[i].x + dt2*(acc[i].x + dt3*jrk[i].x));
pos[i].y += dt*(vel[i].y + dt2*(acc[i].y + dt3*jrk[i].y));
pos[i].z += dt*(vel[i].z + dt2*(acc[i].z + dt3*jrk[i].z));
vel[i].x += dt*(acc[i].x + dt2*jrk[i].x);
vel[i].y += dt*(acc[i].y + dt2*jrk[i].y);
vel[i].z += dt*(acc[i].z + dt2*jrk[i].z);
}
forces(n, pos, vel, acc, jrk, eps2);
if (dt > 0.0)
{
const real h = dt*0.5;
const real hinv = 1.0/h;
const real f1 = 0.5*hinv*hinv;
const real f2 = 3.0*hinv*f1;
const real dt2 = dt *dt * (1.0/2.0);
const real dt3 = dt2*dt * (1.0/3.0);
const real dt4 = dt3*dt * (1.0/4.0);
const real dt5 = dt4*dt * (1.0/5.0);
for (int i = 0; i < n; i++)
{
/* compute snp & crk */
const real4 Am( acc[i].x - acc0[i].x, acc[i].y - acc0[i].y, acc[i].z - acc0[i].z);
const real4 Jm(h*(jrk[i].x - jrk0[i].x), h*(jrk[i].y - jrk0[i].y), h*(jrk[i].z - jrk0[i].z));
const real4 Jp(h*(jrk[i].x + jrk0[i].x), h*(jrk[i].y + jrk0[i].y), h*(jrk[i].z + jrk0[i].z));
real4 snp(f1* Jm.x, f1* Jm.y, f1* Jm.z );
real4 crk(f2*(Jp.x - Am.x), f2*(Jp.y - Am.y), f2*(Jp.z - Am.z));
snp.x -= h*crk.x;
snp.y -= h*crk.y;
snp.z -= h*crk.z;
/* correct */
pos[i].x += dt4*snp.x + dt5*crk.x;
pos[i].y += dt4*snp.y + dt5*crk.y;
pos[i].z += dt4*snp.z + dt5*crk.z;
vel[i].x += dt3*snp.x + dt4*crk.x;
vel[i].y += dt3*snp.y + dt4*crk.y;
vel[i].z += dt3*snp.z + dt4*crk.z;
}
}
return timestep(n, vel, acc, eta, eps2);
}
