#include <massspectrumpluscombiner.h>

Inheritance diagram for pappso::MassSpectrumPlusCombiner:

Public Member Functions
	MassSpectrumPlusCombiner ()
	Construct an uninitialized instance. More...

	MassSpectrumPlusCombiner (int decimal_places)

	MassSpectrumPlusCombiner (const MassSpectrumPlusCombiner &other)

	MassSpectrumPlusCombiner (MassSpectrumPlusCombinerCstSPtr other)

virtual	~MassSpectrumPlusCombiner ()
	Destruct the instance. More...

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. More...

	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. More...

void	setBins (std::vector< pappso_double > bins)

const std::vector< pappso_double > &	getBins () const

std::size_t	binCount () 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`. More...

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) More...

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.

36 {

37 }

◆ MassSpectrumPlusCombiner() [2/4]

pappso::MassSpectrumPlusCombiner::MassSpectrumPlusCombiner ( int decimal_places )

Definition at line 40 of file massspectrumpluscombiner.cpp.

   : MassSpectrumCombiner(decimal_places)
 {
 }

◆ MassSpectrumPlusCombiner() [3/4]

pappso::MassSpectrumPlusCombiner::MassSpectrumPlusCombiner ( const MassSpectrumPlusCombiner & other )

Definition at line 46 of file massspectrumpluscombiner.cpp.

   : MassSpectrumCombiner(other)
  
 {
 }

◆ MassSpectrumPlusCombiner() [4/4]

pappso::MassSpectrumPlusCombiner::MassSpectrumPlusCombiner ( MassSpectrumPlusCombinerCstSPtr other )

Definition at line 54 of file massspectrumpluscombiner.cpp.

   : MassSpectrumCombiner(other)
  
 {
 }

◆ ~MassSpectrumPlusCombiner()

pappso::MassSpectrumPlusCombiner::~MassSpectrumPlusCombiner ( )

virtual

Destruct the instance.

Definition at line 63 of file massspectrumpluscombiner.cpp.

64 {

65 }

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;
  
       //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)
         {
  
           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))
           if(trace_iter->y)
             {
               trace_x = trace_iter->x;
               trace_y = trace_iter->y;
  
               // 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)
                 {
  
                   //qDebug() << "Matched, increment trace_iter";
  
                   new_data_point.y += trace_y;
  
                   // 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
             {
               // 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(1)
  
       // 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 336 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 pappso::MassSpectrumCombiner::m_bins, and pappso::MassDataCombinerInterface::m_decimalPlaces.

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

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

Public Member Functions

Additional Inherited Members