#include <cosinesimilarity.h>

Public Member Functions
	CosineSimilarity (PrecisionPtr precision)
	CosineSimilarity (const CosineSimilarity &other)
	~CosineSimilarity ()
double	similarity (pappso::Trace trace_a, pappso::Trace trace_b) const

Private Attributes
PrecisionPtr	mp_precision
FilterInterfaceSPtr	msp_filterExclusion

Detailed Description

Todo: write docs

Definition at line 43 of file cosinesimilarity.h.

Constructor & Destructor Documentation

◆ CosineSimilarity() [1/2]

CosineSimilarity::CosineSimilarity ( PrecisionPtr precision )

Default constructor

Definition at line 36 of file cosinesimilarity.cpp.

{
  mp_precision = precision;
 
  msp_filterExclusion = std::make_shared<FilterMzExclusion>(precision);
}

References mp_precision, and msp_filterExclusion.

Referenced by CosineSimilarity().

◆ CosineSimilarity() [2/2]

CosineSimilarity::CosineSimilarity ( const CosineSimilarity & other )

Copy constructor

Parameters

other TODO

Definition at line 43 of file cosinesimilarity.cpp.

{
  mp_precision        = other.mp_precision;
  msp_filterExclusion = other.msp_filterExclusion;
}

References CosineSimilarity(), mp_precision, and msp_filterExclusion.

◆ ~CosineSimilarity()

CosineSimilarity::~CosineSimilarity ( )

Destructor

Definition at line 49 of file cosinesimilarity.cpp.

50{

51}

Member Function Documentation

◆ similarity()

double pappso::CosineSimilarity::similarity	(	pappso::Trace	trace_a,
		pappso::Trace	trace_b ) const

Definition at line 54 of file cosinesimilarity.cpp.

{
  // get inner peaks
  // we need a filter to get pairs of common peaks between a & b
  //  or at least compute quickly intensity square of common pairs
 
  msp_filterExclusion.get()->filter(trace_a);
  msp_filterExclusion.get()->filter(trace_b);
 
  auto itb                       = trace_b.begin();
  double inner_intensity_product = 0;
  for(const auto &peak_a : trace_a)
    {
      MzRange range(peak_a.x, mp_precision);
      double low = range.lower();
      double up  = range.upper();
 
      while((itb != trace_b.end()) && (itb->x < low))
        {
          itb++;
        }
      if(itb->x < up)
        {
          inner_intensity_product += peak_a.y * itb->y;
        }
    }
 
  double tracea_product = 0;
  // a intensity sum of intensity square
  for(const auto &peak_a : trace_a)
    {
      tracea_product += peak_a.y * peak_a.y;
    }
 
 
  double traceb_product = 0;
  // a intensity sum of intensity square
  for(const auto &peak_a : trace_b)
    {
      traceb_product += peak_a.y * peak_a.y;
    }
 
  return (inner_intensity_product / (sqrt(tracea_product) * sqrt(traceb_product)));
}

References pappso::MzRange::lower(), mp_precision, msp_filterExclusion, and pappso::MzRange::upper().

Member Data Documentation

◆ mp_precision

PrecisionPtr pappso::CosineSimilarity::mp_precision

private

Definition at line 66 of file cosinesimilarity.h.

Referenced by CosineSimilarity(), CosineSimilarity(), and similarity().

◆ msp_filterExclusion

FilterInterfaceSPtr pappso::CosineSimilarity::msp_filterExclusion