void rice::pastry::testing::ClosestRegrTest::run()
{
for (auto i = int32_t(0); i < NUM_NODES_; i++) {
auto node = npc(factory)->newNode(getBootstrap());
{
synchronized synchronized_0(node);
{
while (!npc(node)->isReady()) {
try {
npc(node)->wait(500);
} catch (::java::lang::InterruptedException* ie) {
return;
}
}
}
}
if(i > 0)
test(i, java_cast< ::rice::pastry::direct::DirectNodeHandle* >(npc(node)->getLocalHandle()));
npc(::java::lang::System::out())->println(::java::lang::StringBuilder().append(u"CREATED NODE "_j)->append(i)
->append(u" "_j)
->append(static_cast< ::java::lang::Object* >(npc(node)->getNodeId()))->toString());
npc(pastryNodes)->add(static_cast< ::java::lang::Object* >(node));
auto ave = getAvgNumEntries(pastryNodes);
npc(::java::lang::System::out())->println(::java::lang::StringBuilder().append(u"Avg Num Entries:"_j)->append(ave)->toString());
}
npc(::java::lang::System::out())->println(::java::lang::StringBuilder().append(u"SO FAR: "_j)->append(incorrect)
->append(u"/"_j)
->append(NUM_NODES_)
->append(u" PERCENTAGE: "_j)
->append((sum / incorrect))->toString());
}
void BrowserManager::Impl::BrowserManagerEntry()
{
std::string bootstrapPath = getBootstrap();
bool thread_exit = false;
PushEvent([] {
CefMainArgs mainArgs;
CefSettings settings;
settings.log_severity = LOGSEVERITY_VERBOSE;
settings.windowless_rendering_enabled = true;
settings.no_sandbox = true;
CefString(&settings.cache_path).FromASCII(obs_module_config_path(""));
CefString(&settings.browser_subprocess_path) = getBootstrap();
CefRefPtr<BrowserApp> app(new BrowserApp());
CefExecuteProcess(mainArgs, app, nullptr);
CefInitialize(mainArgs, settings, app, nullptr);
CefRegisterSchemeHandlerFactory("http", "absolute", new BrowserSchemeHandlerFactory());
CefRunMessageLoop();
CefShutdown();
});
while (true) {
if (os_event_timedwait(dispatchEvent, 10) != ETIMEDOUT) {
pthread_mutex_lock(&dispatchLock);
while (!queue.empty()) {
auto event = queue[0];
event();
queue.erase(queue.begin());
}
thread_exit = !threadAlive;
pthread_mutex_unlock(&dispatchLock);
if (thread_exit) {
return;
}
}
}
}
// perform classification in separate threads
void Classifier::runThread(FastaReader &reader)
{
DnaSequence seq;
boost::mt19937 randGen(0);
RandomGen generator(randGen);
while(seq = reader.readSequence())
{
// reproducible randomness
randGen.seed(reader.numRead());
// get a query sequence and convert to kmers
KmerSequence fwdSeq = kmerizer_.kmerize(seq);
// and the reverse complement
KmerSequence revSeq = kmerizer_.revComp(fwdSeq);
// search against database using both forward and reverse sequences
searchHit fwdHit = referenceData_.search(fwdSeq);
searchHit revHit = referenceData_.search(revSeq);
// use the direction which gave the highest scoring hit
KmerSequence &querySeq = fwdHit.score > revHit.score ? fwdSeq : revSeq;
searchHit &hit = fwdHit.score > revHit.score ? fwdHit : revHit;
std::vector<float> bootstraps(referenceData_.numLevels(), 0.f);
std::vector<std::string> annotations(referenceData_.numLevels(), "AMBIGUOUS");
// make each level annotations into a list of uniques
for (unsigned int i=0; i< hit.annotationIds.size(); i++)
{
std::sort(hit.annotationIds[i].begin(), hit.annotationIds[i].end());
std::vector<unsigned int>::iterator it;
it = std::unique(hit.annotationIds[i].begin(), hit.annotationIds[i].end());
hit.annotationIds[i].resize(std::distance(hit.annotationIds[i].begin(), it));
if (hit.annotationIds[i].size() == 1)
annotations[i] = referenceData_.annotationFromId(*hit.annotationIds[i].begin());
}
// bootstrap
if(numBootstrap_ > 0)
bootstraps = getBootstrap(querySeq, generator, hit);
// output
std::stringstream s;
s << std::setprecision(2) << std::fixed;
s << querySeq.header.substr(0, querySeq.header.find("\t")) << "\t";
s << hit.score << "\t";
//for(unsigned int i=0; i<bootstraps.size(); i++)
unsigned int i=bootstraps.size();
while(i--)
{
s << annotations[i] << "\t";
s << bootstraps[i];
if(i>0)
{
s << "\t";
}
else
{
// dump ambiguous species
if (hit.annotationIds[i].size() > 1 && outputAmbiguous_)
{
s << "\t";
for(std::vector<unsigned int>::iterator it = hit.annotationIds[i].begin(); it != hit.annotationIds[i].end(); ++it)
{
if (it != hit.annotationIds[i].begin())
s << ",";
s << referenceData_.annotationFromId(*it);
}
}
s << std::endl;
}
}
boost::mutex::scoped_lock lock(mutex_);
std::cout << s.str();
}
}
