pappso::MassSpectrumPlusCombiner Class Reference

#include <massspectrumpluscombiner.h>

Inheritance diagram for pappso::MassSpectrumPlusCombiner:

Public Member Functions
Q_INVOKABLE	MassSpectrumPlusCombiner (QObject *parent_p=nullptr)
	Construct an uninitialized instance.
Q_INVOKABLE	MassSpectrumPlusCombiner (int decimal_places, QObject *parent_p=nullptr)
	MassSpectrumPlusCombiner (const MassSpectrumPlusCombiner &other, QObject *parent_p=nullptr)
	MassSpectrumPlusCombiner (MassSpectrumPlusCombinerCstSPtr other, QObject *parent_p=nullptr)
virtual	~MassSpectrumPlusCombiner ()
	Destruct the instance.
MassSpectrumPlusCombiner &	operator= (const MassSpectrumPlusCombiner &other)
virtual Q_INVOKABLE MapTrace &	combine (MapTrace &map_trace, const Trace &trace) const override
virtual Q_INVOKABLE MapTrace &	combine (MapTrace &map_trace_out, const MapTrace &map_trace_in) const override
Public Member Functions inherited from pappso::MassSpectrumCombiner
	MassSpectrumCombiner (QObject *parent_p=nullptr)
	Construct an uninitialized instance.
	MassSpectrumCombiner (int decimal_places, QObject *parent_p=nullptr)
	MassSpectrumCombiner (std::vector< pappso_double > bins, int decimalPlaces=-1, QObject *parent_p=nullptr)
	MassSpectrumCombiner (MassSpectrumCombinerCstSPtr other, QObject *parent_p=nullptr)
	MassSpectrumCombiner (const MassSpectrumCombiner &other, QObject *parent_p=nullptr)
	MassSpectrumCombiner (const MassSpectrumCombiner &&other, QObject *parent_p=nullptr)
virtual	~MassSpectrumCombiner ()
	Destruct the instance.
Q_INVOKABLE void	setBins (std::vector< pappso_double > bins)
Q_INVOKABLE const std::vector< pappso_double > &	getBins () const
Q_INVOKABLE std::size_t	binCount () const
Q_INVOKABLE 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)

Static Public Member Functions
static void	registerJsConstructor (QJSEngine *engine)
Static Public Member Functions inherited from pappso::MassSpectrumCombiner
static void	registerJsConstructor (QJSEngine *engine)

Additional Inherited Members
Public Types inherited from pappso::MassDataCombinerInterface
using	Iterator = std::vector<const Trace *>::const_iterator
Signals inherited from pappso::MassSpectrumCombiner
void	binCountChanged ()
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).
Properties inherited from pappso::MassSpectrumCombiner
int	size

Detailed Description

Definition at line 20 of file massspectrumpluscombiner.h.

Constructor & Destructor Documentation

MassSpectrumPlusCombiner() [1/4]

pappso::MassSpectrumPlusCombiner::MassSpectrumPlusCombiner

(

QObject *

parent_p = nullptr

)

Construct an uninitialized instance.

Definition at line 27 of file massspectrumpluscombiner.cpp.

  : MassSpectrumCombiner(parent_p)
{
}

References pappso::MassSpectrumCombiner::MassSpectrumCombiner().

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

MassSpectrumPlusCombiner() [2/4]

pappso::MassSpectrumPlusCombiner::MassSpectrumPlusCombiner	(	int	decimal_places,
		QObject *	parent_p = nullptr )

Definition at line 32 of file massspectrumpluscombiner.cpp.

  : MassSpectrumCombiner(decimal_places, parent_p)
{
}

References pappso::MassSpectrumCombiner::MassSpectrumCombiner().

MassSpectrumPlusCombiner() [3/4]

pappso::MassSpectrumPlusCombiner::MassSpectrumPlusCombiner	(	const MassSpectrumPlusCombiner &	other,
		QObject *	parent_p = nullptr )

Definition at line 38 of file massspectrumpluscombiner.cpp.

  : MassSpectrumCombiner(other, parent_p)
 
{
}

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

MassSpectrumPlusCombiner() [4/4]

pappso::MassSpectrumPlusCombiner::MassSpectrumPlusCombiner	(	MassSpectrumPlusCombinerCstSPtr	other,
		QObject *	parent_p = nullptr )

Definition at line 45 of file massspectrumpluscombiner.cpp.

  : MassSpectrumCombiner(other, parent_p)
 
{
}

References pappso::MassSpectrumCombiner::MassSpectrumCombiner().

~MassSpectrumPlusCombiner()

pappso::MassSpectrumPlusCombiner::~MassSpectrumPlusCombiner ( )

virtual

Destruct the instance.

Definition at line 53 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;
    }
 
  // 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."));
 
  // qDebug() << qSetRealNumberPrecision(6) << "There are " << m_bins.size() <<
  // "bins running from"
  //          << m_bins.front() << "to" << m_bins.back();
 
  // Since the map_trace argument is used all along the combination of
  // potentially thousands of mass spectra, we need to be careful. But
  // clearly, if that map_trace object is empty, then, one way to accelerate the
  // whole process is to copy the bins in there and later assume that
  // the bin is already in it. So that we need not test each time if we have
  // inserted the new data point or if we simply need to increment its
  // intensity.
 
  if(!map_trace.size())
    {
      std::transform(m_bins.begin(),
                     m_bins.end(),
                     std::inserter(map_trace, map_trace.end()),
                     [](double key) {
                       return std::make_pair(key, 0.0);
                     });
    }
 
  // 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();
 
  // qDebug() << qSetRealNumberPrecision(6) << "The trace to combine has " <<
  // trace.size()
  //          << "data points, with first a m/z" << trace.front().x << "and last
  //          at m/z"
  //          << trace.back().x;
 
  // We will iterate in the destination map_trace that has been filled with
  // the bins initially computed for this combiner.
  using BinIter                  = std::map<double, double>::iterator;
  BinIter map_trace_bin_iter     = map_trace.begin();
  BinIter map_trace_bin_end_iter = map_trace.end();
 
  // We do not want to iterate in too many map_trace items before arriving
  // to the map_trace item that matches the m/z value of the first data
  // point in trace.
 
  // Get the first map_trace bin that would match the very first data point in
  // the trace that we need to combine into the map_trace. We want the first
  // map_trace element having key >= trace_iter->x.
  BinIter map_trace_bin_iter_for_mz = map_trace.upper_bound(trace_iter->x);
 
  // If it's not the beginning, the previous element is what we want
  if(map_trace_bin_iter_for_mz != map_trace.begin())
    {
      map_trace_bin_iter =
        --map_trace_bin_iter_for_mz; // This is the greatest map_trace key <
                                     // trace_iter->x
 
      // qDebug() << "Found map_trace key=" << map_trace_bin_iter_for_mz->first
      //          << ", value=" << map_trace_bin_iter_for_mz->second;
    }
  else
    {
      // qDebug() << "The first bin found to match the first data point in trace
      // is:"
      // << map_trace.begin()->first;
    }
 
  // qDebug() << "The first bin found to match the first m/z value in the trace
  // to combine ("
  //          << trace_iter->x
  //          << ") is at index:" << std::distance(map_trace.begin(),
  //          map_trace_bin_iter);
 
  while(map_trace_bin_iter != map_trace_bin_end_iter)
    {
      // qDebug() << qSetRealNumberPrecision(6)
      //          << "Now iterating in new bin with mz:" <<
      //          map_trace_bin_iter->first
      //          << "at a distance of the first bin:"
      //          << std::distance(map_trace.begin(), map_trace_bin_iter);
 
      // 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()
      //<< "at data point distance from first point in trace:"
 
      while(trace_iter != trace_iter_end)
        {
          // qDebug() << qSetRealNumberPrecision(6)
          //          << "trace data point being iterated into: " <<
          //          trace_iter->x << " - "
          //          << trace_iter->y;
 
          // If trace is not to the end and the y value is not 0, 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(trace_iter->x <= map_trace_bin_iter->first)
            {
              // qDebug() << qSetRealNumberPrecision(6) << "Matched because
              // trace x" << trace_iter->x
              //          << "is <= current bin m/z" <<
              //          map_trace_bin_iter->first;
 
              // qDebug() << "Incrementing the y value by " << trace_iter->y;
 
              map_trace_bin_iter->second += trace_iter->y;
 
              // qDebug() << qSetRealNumberPrecision(6)
              //          << "After incrementation of the intensity: " <<
              //          map_trace_bin_iter->second;
 
              // Because we matched, we can step-up with the
              // trace iterator.  The idea is that, if the bins are large, then,
              // multiple data points from a given mass spec acquisition' trace
              // may fall inside that bin.
 
              // qDebug() << "Now increment the trace iterator.";
 
              ++trace_iter;
            }
          else
            {
              // The trace data point's x did not match the current map_trace
              // bin m/z value because the former was greater than the latter.
 
              // Because the DataPoint instances in the trace are sorted in
              // increasing x order, we know we won't have to add any data point
              // to this bin. So we break this loop, which will increment the
              // map_trace 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)
        {
          // Well, in fact we truly need to exit the loops...
          break;
        }
 
      // qDebug() << "Now increment the bin iterator.";
      ++map_trace_bin_iter;
    }
  // End of
  // while(bin_iter != bin_end_iter)
 
  return map_trace;
}

References pappso::MassSpectrumCombiner::m_bins.

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 276 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 58 of file massspectrumpluscombiner.cpp.

{
  if(this == &other)
    return *this;
 
  MassSpectrumCombiner::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.

registerJsConstructor()

void pappso::MassSpectrumPlusCombiner::registerJsConstructor ( QJSEngine * engine )

static

Definition at line 294 of file massspectrumpluscombiner.cpp.

{
  // qDebug() << "registerJsConstructor for MassSpectrumPlusCombiner to
  // QJSEngine.";
 
  if(engine == nullptr)
    {
      qFatal() << "Cannot register class: engine is null";
    }
 
  // Register the meta object as a constructor
  QJSValue jsMetaObject =
    engine->newQMetaObject(&MassSpectrumPlusCombiner::staticMetaObject);
  engine->globalObject().setProperty("MassSpectrumPlusCombiner", jsMetaObject);
}

---

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

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