OpenMS  3.0.0
IntensityBalanceFilter.h
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31 // $Maintainer: Timo Sachsenberg $
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35 #pragma once
36 
38 
39 #include <map>
40 #include <utility>
41 
42 namespace OpenMS
43 {
52  class OPENMS_DLLAPI IntensityBalanceFilter :
53  public FilterFunctor
54  {
55 
56 public:
57 
58  // @name Constructors and Destructors
59  // @{
62 
65 
67  ~IntensityBalanceFilter() override;
68  // @}
69 
70  // @name Operators
71  // @{
73  IntensityBalanceFilter & operator=(const IntensityBalanceFilter & source);
74  // @}
75 
76  // @name Accessors
77  // @{
79  static FilterFunctor * create() { return new IntensityBalanceFilter(); }
80 
82  template <typename SpectrumType>
83  double apply(SpectrumType & spectrum)
84  {
85  double bands = 10;
86  std::multimap<double, Size> band_intensity;
87  double parentmass = 0.0;
88  if (!spectrum.getPrecursors().empty()) parentmass = spectrum.getPrecursors()[0].getMZ();
89  Size j = 0;
90  for (Size i = 0; i < bands; ++i)
91  {
92  double intensity = 0;
93 
94  //bern 2004 says to only check between 300 and size
95  //but that seems inappropriate for small peptides (smallest is ca 450)
96  while (j < spectrum.size() && spectrum[j].getPosition()[0] < (parentmass - 300) / bands * (i + 1) + 300)
97  {
98  intensity += spectrum[j++].getIntensity();
99  }
100  band_intensity.insert(std::make_pair(intensity, i));
101  }
102  j = 0;
103  double total_intensity = 0;
104  double twobiggest = 0;
105  double sevensmallest = 0;
106  for (std::multimap<double, Size>::reverse_iterator mmrit = band_intensity.rbegin(); mmrit != band_intensity.rend(); ++mmrit, ++j)
107  {
108  total_intensity += mmrit->first;
109  //take the two biggest
110  if (j < 2)
111  {
112  twobiggest += mmrit->first;
113  }
114  //take the seven smallest
115  if (j > 2)
116  {
117  sevensmallest += mmrit->first;
118  }
119  }
120 
121  return (twobiggest - sevensmallest) / total_intensity;
122  }
123 
125  static const String getProductName()
126  {
127  return "IntensityBalanceFilter";
128  }
129 
130  // @}
131 
132  };
133 }
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::SpectrumSettings::getPrecursors
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::IntensityBalanceFilter
IntensityBalanceFilter divides the m/z-range into ten regions and sums the intensity in these regions...
Definition: IntensityBalanceFilter.h:52
FilterFunctor.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::FilterFunctor
A FilterFunctor extracts some spectrum characteristics for quality assessment.
Definition: FilterFunctor.h:44
OpenMS::IntensityBalanceFilter::create
static FilterFunctor * create()
Definition: IntensityBalanceFilter.h:79
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::IntensityBalanceFilter::apply
double apply(SpectrumType &spectrum)
Definition: IntensityBalanceFilter.h:83
OpenMS::IntensityBalanceFilter::getProductName
static const String getProductName()
Definition: IntensityBalanceFilter.h:125