/**
Process HTTP response message from cimserver
@param httpResponse Array<char> reply from cimserver
@param ostream the ostream to which output should be written
@param estream the ostream to which errors should be written
@return true = wait for data from challenge response
@return false = client response has been received
*/
void WbemExecCommand::_handleResponse( Array<char> responseMessage,
ostream& oStream,
ostream& eStream
)
{
String startLine;
Array<HTTPHeader> headers;
Uint32 contentLength;
Uint32 contentOffset = 0;
HTTPMessage* httpMessage;
Boolean needsAuthentication = false;
httpMessage = new HTTPMessage( responseMessage, 0 );
httpMessage->parse( startLine, headers, contentLength );
if( contentLength > 0 )
{
contentOffset = responseMessage.size() - contentLength;
}
else
{
contentOffset = responseMessage.size();
}
String httpVersion;
Uint32 statusCode;
String reasonPhrase;
Boolean parsableMessage = HTTPMessage::parseStatusLine(
startLine, httpVersion, statusCode, reasonPhrase);
if (!parsableMessage || (statusCode != HTTP_STATUSCODE_OK))
{
// Received an HTTP error response
// Output the HTTP error message and exit
for (Uint32 i = 0; i < contentOffset; i++)
{
oStream << responseMessage[i];
}
oStream.flush();
if( contentLength > 0 )
{
_printContent( oStream, responseMessage, contentOffset );
}
exit( 1 );
}
//
// Received a valid HTTP response from the server.
//
if (_debugOutput2)
{
for (Uint32 i = 0; i < contentOffset; i++)
{
oStream << responseMessage[i];
}
oStream.flush();
}
_printContent( oStream, responseMessage, contentOffset );
}
void clustalFormat::write(ostream &out, const sequenceContainer& sd) {
// setting some parameters
const int numOfPositionInLine = 60;
int maxLengthOfSeqName =0;
for (sequenceContainer::constTaxaIterator p=sd.constTaxaBegin(); p != sd.constTaxaEnd(); ++p ) {
int nameLen = (*p).name().size();
if (nameLen>maxLengthOfSeqName) maxLengthOfSeqName=nameLen;
}
if (maxLengthOfSeqName<15) maxLengthOfSeqName=16;
else maxLengthOfSeqName=maxLengthOfSeqName+4; // all this maxLengthOfSeqName is the
out<<"CLUSTAL V"<<endl;
// num. of space after the name.
int currentPosition = 0;
int charLen = sd.seqLen();
//in case of codon alphabet the character length is : 3*(sequence_length)
// codon codonAlph;
if (sd.alphabetSize()>=60) charLen*=3;
out<<endl<<endl;
while (currentPosition < charLen ) {
out.flush();
//for (vector<const sequenceContainer::sequenceDatum*>::const_iterator it5= vec.begin(); it5!=vec.end(); ++ it5) {
for (sequenceContainer::constTaxaIterator it5=sd.constTaxaBegin();it5!=sd.constTaxaEnd();++it5) {
for (int iName = 0 ;iName<maxLengthOfSeqName; ++iName) {
if (iName<(*it5).name().size()) {
out<<(*it5).name()[iName];
out.flush();
}
else out<<" ";
}
out.flush();
out<<" ";
if (charLen<numOfPositionInLine)
out<<it5->toString()<<endl;
else {
for (int k=currentPosition; k < currentPosition+numOfPositionInLine; ++k) {
if (k>=charLen)
break;
out<<it5->toString()[k];
//in case of codon alphabet each position is three characters
if (sd.alphabetSize()>=60){
out<<it5->toString()[++k];
out<<it5->toString()[++k];
}
}
out<<endl;
}
}
currentPosition +=numOfPositionInLine;
out<<endl<<endl;
}
return;
}
void makeArrowObject(ostream& os)
{
GluTriStripAdder adder(&os);
g_adder = &adder;
//float barRadius = 0.7, barLen = 15.0, triStartRadius = 1.5, triLen = 5.0;
//float barRadius = 1.5, barLen = 12.0, triStartRadius = 2.4, triLen = 8.0;
float barRadius = 1, barLen = 13.0, triStartRadius = 2, triLen = 7.0;
int slices = 20;
GLUquadric q;
q.orientation = GLU_OUTSIDE;
sgluCylinder(&q, barRadius, barRadius, barLen, slices, 1);
q.orientation = GLU_INSIDE;
sgluDisk(&q, 0, barRadius, slices, 1);
adder.m_translate.z = barLen;
q.orientation = GLU_OUTSIDE;
sgluCylinder(&q, triStartRadius, 0, triLen, slices, 1);
q.orientation = GLU_INSIDE;
sgluDisk(&q, barRadius, triStartRadius, slices, 1);
os << "\nVTX " << adder.m_addedVtx.size() << endl;
adder.printJs(os);
os.flush();
g_adder = nullptr;
}
void TextWriter::write(ostream & output, map<int, list<Rule> > rules) {
map<int, list<Rule> >::iterator im;
for (im=rules.begin(); im!=rules.end(); ++im) {
output << "====================" << endl;
output << im->second.front().class_attribute.second << ": ";
output << im->second.front().decision << endl;
output << "--------------------" << endl;
list<Rule>::iterator ir;
for (ir=im->second.begin(); ir!=im->second.end(); ++ir) {
map<string, string>::iterator ia;
for (ia=ir->attributes.begin(); ia!=ir->attributes.end(); ++ia) {
if (ia->second == "") continue;
output << ia->first << "(" << ia->second << ")";
if (ir->attributes.size() > 1 && ia!=--ir->attributes.end()) {
output << ", ";
}
}
output << endl;
}
output << endl;
}
output.flush();
}
void despoof::log(ostream &target, int severity, const string &text)
{
auto prev = target.imbue(loglocale());
target << "[" << severitytext(severity) << " " << as::datetime << time(0) << "] " << text << endl;
target.flush();
target.imbue(prev);
}
/** Pop bubbles discovered previously. */
size_t NetworkSequenceCollection::
performNetworkPopBubbles(ostream& out)
{
Timer timer("NetworkPopBubbles");
// Deal with any packets still in the queue. The barrier
// synchronization guarantees that the packets have been
// delivered, but we may not have dealt with them yet.
pumpNetwork();
assert(m_comm.receiveEmpty());
size_t numPopped = 0;
for (BranchGroupMap::iterator iter = m_bubbles.begin();
iter != m_bubbles.end(); iter++) {
assert(iter->second.getStatus() == BGS_JOINED);
// Check whether this bubble has already been popped.
if (!iter->second.isAmbiguous(m_data))
continue;
numPopped++;
AssemblyAlgorithms::writeBubble(out,
iter->second, m_numPopped + numPopped);
AssemblyAlgorithms::collapseJoinedBranches(
this, iter->second);
assert(!iter->second.isAmbiguous(m_data));
assert(m_comm.receiveEmpty());
}
m_bubbles.clear();
out.flush();
assert(out.good());
logger(0) << "Removed " << numPopped << " bubbles.\n";
return numPopped;
}
/**
* Print an FST to an ostream.
* @param fst [in] FST to print.
* @param os [in,out] ostream.
*
* @return 0 on success; negative POSIX error code on error.
*/
int fstPrint(IFst *fst, ostream &os)
{
if (!fst) {
// Invalid parameters.
return -EINVAL;
}
vector<uint8_t> tree_lines;
tree_lines.reserve(16);
FstFileCount fc = {0, 0};
int ret = fstPrint(fst, os, "/", 0, tree_lines, fc);
if (ret != 0) {
return ret;
}
// Print the file count.
// NOTE: Formatting numbers using ostringstream() because
// MSVC's printf() doesn't support thousands separators.
// TODO: CMake checks?
ostringstream dircount, filecount;
dircount << fc.dirs;
filecount << fc.files;
os << '\n' <<
// tr: Parameter is a number; it's formatted elsewhere.
rp_sprintf(NC_("FstPrint", "%s directory", "%s directories", fc.dirs), dircount.str().c_str()) << ", " <<
// tr: Parameter is a number; it's formatted elsewhere.
rp_sprintf(NC_("FstPrint", "%s file", "%s files", fc.files), filecount.str().c_str()) << '\n';
os.flush();
return 0;
}
void PoK_point_Prover::respond(ostream &os, const ZZ_p &chall)
{
if (!announced)
{
throw runtime_error("respond() invoked before announce().");
}
if (responded)
{
throw runtime_error("respond() invoked twice.");
}
ZZ_p fi = eval(com.f, index);
// Compute the responses
ZZ_p u1 = s1 - chall / gamma;
ZZ_p u2 = s2 - fi * chall;
responded = true;
// cout << "p:chall=" << chall << "\n";
// cout << "p:u1 = " << u1 << "\n";
// cout << "p:u2 = " << u2 << "\n";
os << u1 << ' ' << u2;
os.flush();
}
void CsvWriter::write(ostream & output, map<int, list<Rule> > rules) {
// write header
if (rules.empty()) return;
map<string, string>::iterator at;
for (at=rules.begin()->second.front().attributes.begin(); at!=rules.begin()->second.front().attributes.end(); ++at) {
output << at->first << ";";
}
output << rules.begin()->second.front().class_attribute.second << endl;
map<int, list<Rule> >::iterator im;
for (im=rules.begin(); im!=rules.end(); ++im) {
list<Rule>::iterator ir;
for (ir=im->second.begin(); ir!=im->second.end(); ++ir) {
map<string, string>::iterator ia;
for (ia=ir->attributes.begin(); ia!=ir->attributes.end(); ++ia) {
if (ia->second!="") {
output << ia->second;
}
output << ";";
}
output << ir->decision;
output << endl;
}
}
output.flush();
}
void RandomSampleJob::ReportResultsHeader (ostream& r)
{
r << "Job" << "\t"
<< "SVM" << "\t"
<< "Feature" << "\t"
<< "Compresion" << "\t"
<< "" << "\t" // C
<< "" << "\t" // Gamma
<< "Order" << "\t"
<< "Num" << "\t" // Examples
<< "Sample" << "\t" // Sample Accurcay
<< "Support" << "\t"
<< "Train" << "\t"
<< "Test" << "\t"
<< endl;
r << "Id" << "\t"
<< "Kernel" << "\t"
<< "Encoding" << "\t"
<< "Method" << "\t"
<< "C" << "\t"
<< "Gamma" << "\t"
<< "Num" << "\t"
<< "Examples" << "\t"
<< "Accuracy" << "\t" // Sample Accuracy
<< "Points" << "\t"
<< "Time" << "\t" // Train Time
<< "Time" << "\t" // Test Time
<< endl;
r.flush ();
} /* ReportResultsHeader */
//compute union alignment
int prunionalignment(ostream& out,int m,int *a,int n,int* b)
{
ostringstream sout;
for (int j=1; j<=m; j++)
if (a[j])
sout << j-1 << "-" << a[j]-1 << " ";
for (int i=1; i<=n; i++)
if (b[i] && a[b[i]]!=i)
sout << b[i]-1 << "-" << i-1 << " ";
//fix the last " "
string str = sout.str();
if (str.length() == 0)
str = "\n";
else
str.replace(str.length()-1,1,"\n");
out << str;
out.flush();
return 1;
}
streamsize cb::transfer(istream &in, ostream &out, streamsize length,
SmartPointer<TransferCallback> callback) {
char buffer[BUFFER_SIZE];
streamsize total = 0;
while (!in.fail() && !out.fail()) {
in.read(buffer, length ? min(length, BUFFER_SIZE) : BUFFER_SIZE);
streamsize bytes = in.gcount();
out.write(buffer, bytes);
total += bytes;
if (!callback.isNull() && !callback->transferCallback(bytes)) break;
if (length) {
length -= bytes;
if (!length) break;
}
}
out.flush();
if (out.fail() || length) THROW("Transfer failed");
return total;
}
void SubmatrixQueriesTest::multiSizeBenchmarkBestPositionAndSubmatrixQueries(size_t maxNRows, size_t maxNCols, size_t minNRows, size_t minNCols, size_t stepSize, size_t nSamplePerSize, size_t nPosQueries, size_t nSMQueries, ostream &outputStream)
{
size_t nRows = minNRows, nCols = minNCols;
for (; nRows <= maxNRows && nCols <= maxNCols; nRows += stepSize, nCols += stepSize) {
bench_time_t *benchmarks = new bench_time_t [2];
#ifdef __MACH__
benchmarks[0] = 0;
benchmarks[1] = 0;
#else
benchmarks[0].tv_sec = 0; benchmarks[0].tv_nsec = 0;
benchmarks[1].tv_sec = 0; benchmarks[1].tv_nsec = 0;
#endif
cout << "Fastest queries benchmarks for size: " << nRows << " x " << nCols << " ...";
SubmatrixQueriesTest::multipleBenchmarkBestPositionAndSubmatrixQueries(nRows,nCols, nSamplePerSize, nPosQueries, nSMQueries, benchmarks, benchmarks+1);
cout << " done\n";
outputStream << ((int)nRows) << " ; " << benchTimeAsMiliSeconds(benchmarks[0]) << " ; " << benchTimeAsMiliSeconds(benchmarks[1]) << "\n";
outputStream.flush();
delete [] benchmarks;
}
}
void Shard::printShardInfo( ostream& out ) {
vector<Shard> all;
staticShardInfo.getAllShards( all );
for ( unsigned i=0; i<all.size(); i++ )
out << all[i].toString() << "\n";
out.flush();
}
//------------------------------------------------------------------------//
bool TokenFile::Write(ostream &Output, TokenList* pTokenList, DWORD dwFlags)
{
Clear();
if(dwFlags & TF_CASE_SENSITIVE)
m_bCaseSensitive = true;
else
m_bCaseSensitive = false;
// clear the queue
while(!m_queBuffer.empty())
m_queBuffer.pop();
m_pTokenList = pTokenList;
WriteHeader();
GenerateTables();
WriteTables();
WriteTokens();
while(!m_queBuffer.empty())
{
Output.put(m_queBuffer.front());
m_queBuffer.pop();
}
Output.flush();
return true;
}
/**
* This function write a batch on the standart output it is suposed to
* be read by the function BatchR::inputR
*/
void BatchR::outputR(ostream &f) {
unsigned long int check = 8427; //magic value
f.write(reinterpret_cast<char*>(&check),sizeof(check));
f.write(reinterpret_cast<char*>(&I),sizeof(I));
f.write(reinterpret_cast<char*>(&Isucc),sizeof(Isucc));
size_t v = Mean.size();
f.write(reinterpret_cast<char*>(&v),sizeof(size_t));
v = bernVar.size();
f.write(reinterpret_cast<char*>(&v),sizeof(size_t));
for(unsigned int i =0; i< Mean.size(); i++){
bool tmpbool = IsBernoulli[i];
f.write(reinterpret_cast<char*>(&tmpbool),sizeof(bool));
f.write(reinterpret_cast<char*>(&Mean[i]),sizeof(Mean[0]));
f.write(reinterpret_cast<char*>(&M2[i]),sizeof(Mean[0]));
f.write(reinterpret_cast<char*>(&M3[i]),sizeof(Mean[0]));
f.write(reinterpret_cast<char*>(&M4[i]),sizeof(Mean[0]));
f.write(reinterpret_cast<char*>(&Min[i]),sizeof(Mean[0]));
f.write(reinterpret_cast<char*>(&Max[i]),sizeof(Mean[0]));
}
for(unsigned int i =0; i< bernVar.size(); i++)
f.write(reinterpret_cast<char*>(&bernVar[i]),sizeof(bernVar[0]));
f.write(reinterpret_cast<char*>(&simTime),sizeof(simTime));
f.flush();
}
void
ProfileWriter::DumpProfileHeader(ostream& os)
{
os << "<?xml version=\"1.0\"?>" << endl;
os << "<!DOCTYPE PROFILE [\n" << PROFILEdtd << "]>" << endl;
os.flush();
}
void WordIndex::traverseWords (
BSTNode< MapNode<string, OccurrenceSet> >* node
, ostream & stream
) {
if (NULL == node) {
return;
}
if (NULL != node->GetLeft()) {
traverseWords(node->GetLeft(), stream);
}
if (NULL != node->GetRight()) {
traverseWords(node->GetRight(), stream);
}
stream << (" <word>\n");
stream << (" <value>");
stream.flush();
try {
stream << StringUtil::EncodeToXmlCopy(node->GetValue().GetKey());
} catch (CS240Exception & exception) {
cout << exception.GetMessage() << endl;
}
stream << ("</value>\n");
traverseOccurrences(node->GetValue().GetValue().GetRoot(), stream);
stream << (" </word>\n");
}
void SkippingDisabledBlock(NxsString blockName)
{
if (outf != 0L)
{
*outf << "[!Skipping disabled block (" << blockName << ")...]\n";
outf->flush();
}
}
void SkippingBlock(NxsString blockName)
{
if (outf != 0L)
{
*outf << "[!Skipping unknown block (" << blockName << ")...]\n";
outf->flush();
}
}
inline void printEnd(const char *str=NULL) {
if (o == NULL) return;
if (str != NULL) *o<<str;
*o<<endl;
if (dlm == NULL) {
o->flush();
}
}
bool Properties::save(ostream &os)
{
StringMap::const_iterator iter = m_map.begin();
for (; iter != m_map.end(); ++iter) {
os << iter->first << "=" << iter->second << '\n';
}
os.flush();
return true;
}
void absref_transmit::print(ostream& file, int l) const {
if (l > 0) {
Ifile<<"absref_transmit::print(l="<<l<<") qaref="<<qaref
<<" qaref_pointer="<<qaref_pointer
<<" qaref_other="<<qaref_other
<<"\n";
file.flush();
}
}
void BooleanDAG::mrprint(ostream& out){
out<<"dag "<< this->get_name()<<" :"<<endl;
for(int i=0; i<nodes.size(); ++i){
if(nodes[i] != NULL){
out<<nodes[i]->mrprint()<<endl;
}
}
out.flush();
}
/****************************************************************
* Function for displaying the board.
**/
void Board::display(ostream& outStream)
{
int count = ZERO;
int count2 = ZERO;
outStream << "**************************************************" << endl;
for(int row = ZERO; row < NINE; ++row)
{
for(int col = ZERO; col < NINE; ++col)
{
vector<int> theRow = this->theBoard[row];
if(DUMMY == theRow[col])
{
outStream << " . ";
outStream.flush();
}
else
{
outStream << " " << theRow[col] << " ";
outStream.flush();
}
count++;
if((0 == count%THREE) && (col < NINE))
{
outStream << "|";
outStream.flush();
}
} // for(int col = ONE; col <= NINE; ++col)
outStream << endl;
outStream.flush();
count2++;
if((0 == count2%THREE) && (row < NINE))
{
outStream << "---------|---------|---------" << endl;
outStream.flush();
}
} // for(int row = ONE; row <= NINE; ++row)
outStream << "**************************************************" << endl;
} // void Board::display()
// writes all summary statistics on one single line
// in the same order as that provided by the header
void Trace(ostream& os) {
os << GetLogPrior() << '\t' << GetLogLikelihood() << '\t' << GetLength();
os << '\t' << lambda->val();
os << '\t' << alpha->val();
os << '\t' << GetMeanRate();
os << '\t' << GetVarRate();
os << '\t' << stationary->val().GetEntropy();
os << '\t' << relrate->val().GetMean() << '\t' << relrate->val().GetEntropy();
os << '\n';
os.flush();
}
void Mangrove_PluginMetadata::debug(ostream &os)
{
/* Now, we export the debug representation of the current metadata. */
assert(os.good());
os<<endl<<endl;
os<<"\tThe dynamic plugin of interest has been written and created by ";
if(this->getCAuthor().empty()==true) os<<"<not set>"<<endl;
else os<<this->getCAuthor()<<endl;
os<<"\tLast version: ";
if(this->getCVersion().empty()==true) os<<"<not set>"<<endl;
else os<<this->getCVersion()<<endl;
os<<"\tThe dynamic plugin of interest is described by the ";
if(this->getCSmartClassName().empty()==true) os<<"<not set> smart class, ";
else os<<"'"<<this->getCSmartClassName()<<"' smart class, ";
os<<"which may create:"<<endl<<endl;
os<<"\t\tinstances of the ";
if(this->getCVirtualPluginName().empty()==true) os<<"<not set> class";
else os<<"'"<<this->getCVirtualPluginName()<<"' class";
os<<" as the Virtual Plugin"<<endl;
os<<"\t\tinstances of the ";
if(this->getCTemplatePluginName().empty()==true) os<<"<not set> class";
else os<<"'"<<this->getCTemplatePluginName()<<"' class";
os<<" as the Template Plugin"<<endl<<endl;
os.flush();
os<<"\tThe current dynamic plugin has ";
if(this->getCBaseName().empty()==true) os<<"<not set>";
else os<<"'"<<this->getCBaseName()<<"'";
os<<" as the basename for the corresponding library"<<endl;
os<<"\tThe current dynamic plugin has ";
if(this->getCUniqueIdentifier().empty()==true) os<<"<not set>";
else os<<"'"<<this->getCUniqueIdentifier()<<"'";
os<<" as the unique identifier"<<endl<<endl;
os.flush();
os<<"\tThe current dynamic plugin is specialized for modeling ";
if(this->getCPluginType()==MANGROVE_PLUGIN_IO_COMPONENT) os<<"a soup of the top topological entities"<<endl<<endl;
else if(this->getCPluginType()==MANGROVE_PLUGIN_MANGROVE) os<<"a mangrove, describing a specific topological data structure"<<endl<<endl;
else if(this->getCPluginType()==MANGROVE_PLUGIN_MANGROVE_BUILDER) os<<"a component for constructing a specific mangrove from a soup of the top topological entities"<<endl<<endl;
else { os<<"an unknown task."<<endl<<endl; }
os.flush();
}
void NexusError(NxsString msg, file_pos pos, long line, long col)
{
cerr << "\nError found at line " << line << ", column " << col ;
cerr << " (file position " << pos << "):\n" << msg << endl;
if (outf != 0L)
{
*outf << "\nError found at line " << line << ", column " << col ;
*outf << " (file position " << pos << "):\n" << msg;
outf->flush();
}
exit(2);
}
void CSimulation::print_pos(ostream &pos_stream) {
for (vector<CPlanet>::iterator it = m_SS.m_planets.begin();
it < m_SS.m_planets.end(); it++) {
pos_stream << (*(it->getDynamicsPtr())).m_position << endl;
}
for (vector<CSatellite>::iterator it = m_SS.m_sats.begin();
it < m_SS.m_sats.end(); it++) {
pos_stream << (*(it->getDynamicsPtr())).m_position << endl;
}
pos_stream << "-\n";
pos_stream.flush();
}
void ContextImpl::createCheckpoint(ostream& stream) {
stream.write(CHECKPOINT_MAGIC_BYTES, sizeof(CHECKPOINT_MAGIC_BYTES)/sizeof(CHECKPOINT_MAGIC_BYTES[0]));
writeString(stream, getPlatform().getName());
int numParticles = getSystem().getNumParticles();
stream.write((char*) &numParticles, sizeof(int));
int numParameters = parameters.size();
stream.write((char*) &numParameters, sizeof(int));
for (map<string, double>::const_iterator iter = parameters.begin(); iter != parameters.end(); ++iter) {
writeString(stream, iter->first);
stream.write((char*) &iter->second, sizeof(double));
}
updateStateDataKernel.getAs<UpdateStateDataKernel>().createCheckpoint(*this, stream);
stream.flush();
}
