ValueMap Configure::ReadConfig()
{
ValueMap vals;
vals.clear();
std::ifstream ifs_(conf_path_.c_str(), std::ios::in);
std::string line;
while(std::getline(ifs_, line))
{
std::string name = line.substr(0, line.find_first_of(":"));
if (name.empty() || name == line) continue;
std::string buf(line.substr(line.find_first_of(":")+1));
std::istringstream ss(buf.substr(buf.find_first_of("-0123456789")));
double value;
ss >> value;
vals[name] = value;
}
ifs_.close();
return vals;
}
Forest(const char * _forest_filename_ )
:num_predictors_(0)
{
std::ifstream ifs_(_forest_filename_, std::iostream::in);
if ( ifs_.is_open() )
{
const int kbufferlen = 1024;
char buffer_[kbufferlen];
while ( ifs_.good() )
{
bzero( buffer_, kbufferlen );
ifs_.getline( buffer_, kbufferlen );
PerishableStringTokenizer tokenizer_ ( buffer_, kbufferlen );
const std::vector< const char * > & tokens_ = tokenizer_.GetTokens();
if ( tokens_.empty() ) { continue; }
if ( strcmp(tokens_[0],"NUM_PREDICTORS")==0 && tokens_.size() >= 2 )
{
num_predictors_ = atoi(tokens_[1]);
}
else if ( strcmp(tokens_[0],"TREESTART")==0 )
{
tree_vec_.push_back(Tree());
}
else if ( strcmp(tokens_[0],"TREELINE")==0 && tokens_.size() >= 9 )
{
if ( ! tree_vec_.empty() )
{
Tree & this_tree_ = tree_vec_[tree_vec_.size()-1];
this_tree_.push_back( Node(tokens_,this_tree_.size()) );
}
}
}
ifs_.close();
}
else
{
std::cerr << "ERROR: Cannot open " << _forest_filename_ << " for reading." << std::endl;
exit ( 0 ) ;
}
}
OpenSwath::SpectrumPtr SpectrumAccessOpenMSCached::getSpectrumById(int id) const
{
if (cache_.getSpectraIndex().empty())
{
// remove const from the cache since we need to recalculate the index
// and re-read the data.
(const_cast<CachedmzML*>(&cache_))->createMemdumpIndex(filename_cached_);
}
OpenSwath::BinaryDataArrayPtr mz_array(new OpenSwath::BinaryDataArray);
OpenSwath::BinaryDataArrayPtr intensity_array(new OpenSwath::BinaryDataArray);
int ms_level = -1;
double rt = -1.0;
// FEATURE check if we can keep the filestream open -> risky if someone else
// accesses the file in the meantime
std::ifstream ifs_((filename_cached_).c_str(), std::ios::binary);
ifs_.seekg(cache_.getSpectraIndex()[id]);
cache_.readSpectrumFast(mz_array, intensity_array, ifs_, ms_level, rt);
OpenSwath::SpectrumPtr sptr(new OpenSwath::Spectrum);
sptr->setMZArray(mz_array);
sptr->setIntensityArray(intensity_array);
return sptr;
}
OpenSwath::ChromatogramPtr SpectrumAccessOpenMSCached::getChromatogramById(int id) const
{
if (cache_.getChromatogramIndex().empty())
{
// remove const from the cache since we need to recalculate the index
// and re-read the data.
(const_cast<CachedmzML*>(&cache_))->createMemdumpIndex(filename_cached_);
}
OpenSwath::BinaryDataArrayPtr rt_array(new OpenSwath::BinaryDataArray);
OpenSwath::BinaryDataArrayPtr intensity_array(new OpenSwath::BinaryDataArray);
std::ifstream ifs_((filename_cached_).c_str(), std::ios::binary);
ifs_.seekg(cache_.getChromatogramIndex()[id]);
cache_.readChromatogramFast(rt_array, intensity_array, ifs_);
// push back rt first, then intensity.
// FEATURE (hroest) annotate which is which
std::vector<OpenSwath::BinaryDataArrayPtr> binaryDataArrayPtrs;
binaryDataArrayPtrs.push_back(rt_array);
binaryDataArrayPtrs.push_back(intensity_array);
OpenSwath::ChromatogramPtr cptr(new OpenSwath::Chromatogram);
cptr->binaryDataArrayPtrs = binaryDataArrayPtrs;
return cptr;
}
