void Pipeline::run()
{
while (!pipelineQueue_.empty()) {
Request tempReq = requestQueue_.front();
std::string tempStr;
if (Pipeline::getTraceFlag()) {
if (tempReq.getType() == libpipe::Request::UPDATE) {
tempStr = "Starting Update Request";
} else if (tempReq.getType() == libpipe::Request::DELETE) {
tempStr = "Starting Delete Request";
}
}
LIBPIPE_PIPELINE_TRACE(tempStr);
#ifdef ENABLE_THREADING
boost::exception_ptr error;
pipelineQueue_.front()->processThreadedRequest(tempReq, error);
if (error) {
boost::rethrow_exception(error);
}
#else
pipelineQueue_.front()->processRequest(tempReq);
#endif
pipelineQueue_.pop();
requestQueue_.pop();
}
}
void update(libpipe::Request& req)
{
boost::shared_ptr<libpipe::rtc::SharedData<mgf::MgfFile> > mgfInputFile =
boost::dynamic_pointer_cast<
libpipe::rtc::SharedData<mgf::MgfFile> >(
this->getPort("MGFInputFile"));
boost::shared_ptr<libpipe::rtc::SharedData<mgf::MgfFile> > mgfParsedFile =
boost::dynamic_pointer_cast<
libpipe::rtc::SharedData<mgf::MgfFile> >(
this->getPort("MGFParsedFile"));
LIBPIPE_PIPELINE_TRACE(req, "Starting TopXInYRegions");
mgfInputFile->shared_lock();
mgfParsedFile->lock();
// copy the file so that input is not changed.
mgfParsedFile->set(new mgf::MgfFile(*mgfInputFile->get()));
mgfInputFile->unlock();
// Top X in Y regions
for (mgf::MgfFile::iterator i = mgfParsedFile->get()->begin();
i != mgfParsedFile->get()->end(); ++i) {
// get a temporary object and make sure it is big enough
mgf::MgfSpectrum m;
m.resize(2 * i->size());
// get the top X in Y regions, including duplicated from overlaps
mgf::MgfSpectrum::iterator sEnd = run(i->begin(), i->end(),
m.begin(), LessThanMass(), LessThanAbundance());
// make sure we have enough space in the original object
i->resize(std::distance(m.begin(), sEnd));
// unique copy expectes a sorted range
std::sort(m.begin(), sEnd, LessThanMass());
// copy all unique peaks back into the original MgfSpectrum
mgf::MgfSpectrum::iterator iEnd = std::unique_copy(m.begin(),
sEnd, i->begin());
// crop to fit
i->resize(std::distance(i->begin(), iEnd));
}
mgfParsedFile->unlock();
LIBPIPE_PIPELINE_TRACE(req, "TopXInYRegions is finished");
}
