pappso::MassSpectrumPlusCombiner Class Reference

#include <massspectrumpluscombiner.h>

Inheritance diagram for pappso::MassSpectrumPlusCombiner:

Public Member Functions
	MassSpectrumPlusCombiner ()
	Construct an uninitialized instance.
	MassSpectrumPlusCombiner (int decimal_places)
	MassSpectrumPlusCombiner (const MassSpectrumPlusCombiner &other)
	MassSpectrumPlusCombiner (MassSpectrumPlusCombinerCstSPtr other)
virtual	~MassSpectrumPlusCombiner ()
	Destruct the instance.
MassSpectrumPlusCombiner &	operator= (const MassSpectrumPlusCombiner &other)
virtual MapTrace &	combine (MapTrace &map_trace, const Trace &trace) const override
virtual MapTrace &	combine (MapTrace &map_trace_out, const MapTrace &map_trace_in) const override
Public Member Functions inherited from pappso::MassSpectrumCombiner
	MassSpectrumCombiner ()
	Construct an uninitialized instance.
	MassSpectrumCombiner (int decimal_places)
	MassSpectrumCombiner (std::vector< pappso_double > bins, int decimalPlaces=-1)
	MassSpectrumCombiner (MassSpectrumCombinerCstSPtr other)
	MassSpectrumCombiner (const MassSpectrumCombiner &other)
	MassSpectrumCombiner (const MassSpectrumCombiner &&other)
virtual	~MassSpectrumCombiner ()
	Destruct the instance.
void	setBins (std::vector< pappso_double > bins)
const std::vector< pappso_double > &	getBins () const
std::size_t	binCount () const
QString	binsAsString () const
Public Member Functions inherited from pappso::MassDataCombinerInterface
	MassDataCombinerInterface (int decimal_places=-1)
virtual	~MassDataCombinerInterface ()
void	setDecimalPlaces (int value)
int	getDecimalPlaces () const
virtual MapTrace &	combine (MapTrace &map_trace, Iterator begin, Iterator end)

Additional Inherited Members
Public Types inherited from pappso::MassDataCombinerInterface
using	Iterator = std::vector<const Trace *>::const_iterator
Protected Member Functions inherited from pappso::MassSpectrumCombiner
std::vector< pappso_double >::iterator	findBin (pappso_double mz)
	Find the bin that will contain mz.
Protected Attributes inherited from pappso::MassSpectrumCombiner
std::vector< pappso_double >	m_bins
Protected Attributes inherited from pappso::MassDataCombinerInterface
int	m_decimalPlaces = -1
	Number of decimals to use for the keys (x values)

Detailed Description

Definition at line 24 of file massspectrumpluscombiner.h.

Constructor & Destructor Documentation

MassSpectrumPlusCombiner() [1/4]

pappso::MassSpectrumPlusCombiner::MassSpectrumPlusCombiner

(

)

Construct an uninitialized instance.

Definition at line 35 of file massspectrumpluscombiner.cpp.

{
}

Referenced by MassSpectrumPlusCombiner(), and operator=().

MassSpectrumPlusCombiner() [2/4]

pappso::MassSpectrumPlusCombiner::MassSpectrumPlusCombiner

(

int

decimal_places

)

Definition at line 40 of file massspectrumpluscombiner.cpp.

  : MassSpectrumCombiner(decimal_places)
{
}

References pappso::MassSpectrumCombiner::MassSpectrumCombiner().

MassSpectrumPlusCombiner() [3/4]

pappso::MassSpectrumPlusCombiner::MassSpectrumPlusCombiner

(

const MassSpectrumPlusCombiner &

other

)

Definition at line 46 of file massspectrumpluscombiner.cpp.

  : MassSpectrumCombiner(other)
 
{
}

References pappso::MassSpectrumCombiner::MassSpectrumCombiner(), and MassSpectrumPlusCombiner().

MassSpectrumPlusCombiner() [4/4]

pappso::MassSpectrumPlusCombiner::MassSpectrumPlusCombiner

(

MassSpectrumPlusCombinerCstSPtr

other

)

Definition at line 54 of file massspectrumpluscombiner.cpp.

  : MassSpectrumCombiner(other)
 
{
}

References pappso::MassSpectrumCombiner::MassSpectrumCombiner().

~MassSpectrumPlusCombiner()

pappso::MassSpectrumPlusCombiner::~MassSpectrumPlusCombiner ( )

virtual

Destruct the instance.

Definition at line 63 of file massspectrumpluscombiner.cpp.

{
}

Member Function Documentation

combine() [1/2]

MapTrace & pappso::MassSpectrumPlusCombiner::combine ( MapTrace & map_trace, const Trace & trace ) const

overridevirtual

Implements pappso::MassDataCombinerInterface.

Definition at line 90 of file massspectrumpluscombiner.cpp.

{
  // qDebug();
 
  // If there is no single point in the trace we need to combine into the
  // map_trace, then there is nothing to do.
  if(!trace.size())
    {
      // qDebug() << "Thread:" << QThread::currentThreadId()
      //<< "Returning right away because trace is empty.";
      return map_trace;
    }
 
  // We will need to only use these iterator variables if we do not want to
  // loose consistency.
 
  using TraceIter            = std::vector<DataPoint>::const_iterator;
  TraceIter trace_iter_begin = trace.begin();
  TraceIter trace_iter       = trace_iter_begin;
  TraceIter trace_iter_end   = trace.end();
 
  // The destination map trace will be filled-in with the result of the
  // combination.
 
  // Sanity check:
  if(!m_bins.size())
    throw(ExceptionNotPossible("The bin vector cannot be empty."));
 
  using BinIter = std::vector<pappso_double>::const_iterator;
 
  BinIter bin_iter     = m_bins.begin();
  BinIter bin_end_iter = m_bins.end();
 
  // qDebug() << "initial bins iter at a distance of:"
  //<< std::distance(m_bins.begin(), bin_iter)
  //<< "bins distance:" << std::distance(m_bins.begin(), m_bins.end())
  //<< "bins size:" << m_bins.size() << "first bin:" << m_bins.front()
  //<< "last bin:" << m_bins.back();
 
  // Iterate in the vector of bins and for each bin check if there are matching
  // data points in the trace.
 
  pappso_double current_bin_mz = 0;
 
  pappso_double trace_x = 0;
  pappso_double trace_y = 0;
 
  // Lower bound returns an iterator pointing to the first element in the
  // range [first, last) that is not less than (i.e. greater or equal to)
  // value, or last if no such element is found.
 
  auto bin_iter_for_mz = lower_bound(bin_iter, bin_end_iter, trace_iter->x);
 
  if(bin_iter_for_mz != bin_end_iter)
    {
      if(bin_iter_for_mz != m_bins.begin())
        bin_iter = --bin_iter_for_mz;
    }
  else
    throw(ExceptionNotPossible("The bin vector must match the mz value."));
 
  while(bin_iter != bin_end_iter)
    {
      current_bin_mz = *bin_iter;
 
      // std::cout << std::setprecision(10) << "current bin: " << current_bin_mz
      //<< std::endl;
 
      // qDebug() << "Current bin:"
      //<< QString("%1").arg(current_bin_mz, 0, 'f', 15)
      //<< "at a distance of:"
      //<< std::distance(m_bins.begin(), bin_iter);
 
      // For the current bin, we start by instantiating a new DataPoint. By
      // essence, each bin will have at most one corresponding DataPoint.
 
      DataPoint new_data_point;
 
      // Do not set the y value to 0 so that we can actually test if the
      // data point is valid later on (try not to push back y=0 data
      // points).
      new_data_point.x = current_bin_mz;
 
      // Now perform a loop over the data points in the mass spectrum.
 
      // qDebug() << "Start looping in the trace to check if its DataPoint.x "
      //"value matches that of the current bin."
      //<< "trace_iter:" << trace_iter->toString()
      //<< "data point distance:"
      //<< std::distance(trace_iter_begin, trace_iter);
 
      while(trace_iter != trace_iter_end)
        {
          // std::cout << std::setprecision(10)
          //<< "trace data point being iterated into: " << trace_iter->x
          //<< " - " << trace_iter->y << std::endl;
 
          bool trace_matched = false;
 
          // If trace is not to the end and the y value is not 0
          // apply the shift, perform the rounding and check if the obtained
          // x value is in the current bin, that is if it is less or equal
          // to the current bin.
 
          // qDebug() << "Thread:" << QThread::currentThreadId();
          // qDebug() << "trace_iter:" << trace_iter->toString()
          //<< "data point distance:"
          //<< std::distance(trace_iter_begin, trace_iter);
 
          // if(!Utils::almostEqual(trace_iter->y, 0.0, 10))
 
          trace_x = trace_iter->x;
          trace_y = trace_iter->y;
 
          if(trace_y)
            {
 
              // FIXME: unbelievable behaviour: when building in release mode
              // this code, under i386 (but not x86_64), this code fails if the
              // following%S statement is missing. There are a variety of
              // variants that work, the common denominator being that trace_x
              // has to be output along with a string.
 
              // std::cout << std::setprecision(10)
              //<< "iterated trace point: " << trace_x << " - "
              //<< trace_y << std::endl;
 
              // For this reason I had to deactivate the related tests
              // for i386 in tests/test_massspectrumcombiner.cpp
 
              // trace_x is the m/z value that we need to combine,
              // so make sure we check if there is a mz shift to apply.
 
              // if(m_mzIntegrationParams.m_applyMzShift)
              // trace_x += m_mzIntegrationParams.m_mzShift;
 
              // Now apply the rounding (if any).
              if(m_decimalPlaces != -1)
                trace_x = Utils::roundToDecimals(trace_x, m_decimalPlaces);
 
              if(trace_x <= current_bin_mz)
                {
 
                  // std::cout
                  //<< std::setprecision(10)
                  //<< "Matched, because trace point.x is <= the current "
                  //"bin; increment trace_iter"
                  //<< std::endl;
 
                  new_data_point.y += trace_y;
 
                  // std::cout << std::setprecision(10)
                  //<< "After incrementation of the intensity: "
                  //<< new_data_point.y << std::endl;
 
                  // Let's record that we matched.
                  trace_matched = true;
 
                  // Because we matched, we can step-up with the
                  // iterator.
                  ++trace_iter;
                }
              // else
              //{
              // We did have a non-0 y value, but that did not
              // match. So we do not step-up with the iterator.
              //}
            }
          // End of
          // if(trace_iter->y)
          else
            {
              // std::cout << std::setprecision(10)
              //<< "itered trace point intensity is 0: " << trace_x
              //<< " - " << trace_y << std::endl;
 
 
              // We iterated into a y=0 data point, so just skip it. Let
              // the below code think that we have matched the point and
              // iterate one step up.
 
              // qDebug() << "The y value is almost equal to 0, increment the "
              //"trace iter but do nothing else.";
 
              trace_matched = true;
              ++trace_iter;
            }
          // At this point, check if none of them matched.
 
          if(!trace_matched)
            {
              // None of the first and trace mass spectra data
              // points were found to match the current bin. All we
              // have to do is go to the next bin. We break and the
              // bin vector iterator will be incremented.
 
              // However, if we had a valid new data point, that
              // data point needs to be pushed back in the new mass
              // spectrum.
 
              if(new_data_point.isValid())
                {
 
                  // We need to check if that bin value is present already in
                  // the map_trace object passed as parameter.
 
                  std::pair<std::map<pappso_double, pappso_double>::iterator,
                            bool>
                    result =
                      map_trace.insert(std::pair<pappso_double, pappso_double>(
                        new_data_point.x, new_data_point.y));
 
                  if(!result.second)
                    {
                      // The key already existed! The item was not inserted. We
                      // need to update the value.
 
                      result.first->second += new_data_point.y;
 
                      // qDebug()
                      //<< "Incremented the data point in the map trace.";
                    }
                  // else
                  //{
                  // qDebug()
                  //<< "Inserted a new data point into the map trace.";
                  //}
                }
 
              // We need to break this loop! That will increment the
              // bin iterator.
 
              break;
            }
        }
      // End of
      // while(trace_iter != trace_iter_end)
 
      // Each time we get here, that means that we have consumed all
      // the mass spectra data points that matched the current bin.
      // So go to the next bin.
 
      if(trace_iter == trace_iter_end)
        {
 
          // Make sure a last check is done in case one data point was
          // cooking...
 
          if(new_data_point.isValid())
            {
 
              std::pair<std::map<pappso_double, pappso_double>::iterator, bool>
                result =
                  map_trace.insert(std::pair<pappso_double, pappso_double>(
                    new_data_point.x, new_data_point.y));
 
              if(!result.second)
                {
                  result.first->second += new_data_point.y;
                }
            }
 
          // Now truly exit the loops...
          break;
        }
 
      ++bin_iter;
    }
  // End of
  // while(bin_iter != bin_end_iter)
 
  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()"
  //<< "The combination result mass spectrum being returned has TIC:"
  //<< new_trace.sumY();
 
  return map_trace;
}

References pappso::DataPoint::isValid(), pappso::MassSpectrumCombiner::m_bins, pappso::MassDataCombinerInterface::m_decimalPlaces, pappso::Utils::roundToDecimals(), pappso::DataPoint::x, and pappso::DataPoint::y.

Referenced by combine().

combine() [2/2]

MapTrace & pappso::MassSpectrumPlusCombiner::combine ( MapTrace & map_trace_out, const MapTrace & map_trace_in ) const

overridevirtual

Implements pappso::MassDataCombinerInterface.

Definition at line 370 of file massspectrumpluscombiner.cpp.

{
  // qDebug();
 
  if(!map_trace_in.size())
    {
      // qDebug() << "Thread:" << QThread::currentThreadId()
      //<< "Returning right away because map_trace_in is empty.";
      return map_trace_out;
    }
 
  Trace trace(map_trace_in);
 
  return combine(map_trace_out, trace);
}

References combine().

operator=()

MassSpectrumPlusCombiner & pappso::MassSpectrumPlusCombiner::operator=

(

const MassSpectrumPlusCombiner &

other

)

Definition at line 69 of file massspectrumpluscombiner.cpp.

{
  if(this == &other)
    return *this;
 
  m_decimalPlaces = other.m_decimalPlaces;
 
  m_bins.assign(other.m_bins.begin(), other.m_bins.end());
 
  return *this;
}

References MassSpectrumPlusCombiner(), pappso::MassSpectrumCombiner::m_bins, and pappso::MassDataCombinerInterface::m_decimalPlaces.

---

The documentation for this class was generated from the following files:

• pappsomspp/core/processing/combiners/massspectrumpluscombiner.h
• pappsomspp/core/processing/combiners/massspectrumpluscombiner.cpp