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IntensityBalanceFilter.h
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35 #ifndef OPENMS_FILTERING_TRANSFORMERS_INTENSITYBALANCEFILTER_H
36 #define OPENMS_FILTERING_TRANSFORMERS_INTENSITYBALANCEFILTER_H
37 
39 
40 #include <map>
41 #include <utility>
42 
43 namespace OpenMS
44 {
53  class OPENMS_DLLAPI IntensityBalanceFilter :
54  public FilterFunctor
55  {
56 
57 public:
58 
59  // @name Constructors and Destructors
60  // @{
63 
66 
68  virtual ~IntensityBalanceFilter();
69  // @}
70 
71  // @name Operators
72  // @{
74  IntensityBalanceFilter & operator=(const IntensityBalanceFilter & source);
75  // @}
76 
77  // @name Accessors
78  // @{
80  static FilterFunctor * create() { return new IntensityBalanceFilter(); }
81 
83  template <typename SpectrumType>
84  double apply(SpectrumType & spectrum)
85  {
86  double bands = 10;
87  std::multimap<double, Size> band_intensity;
88  double parentmass = 0.0;
89  if (!spectrum.getPrecursors().empty()) parentmass = spectrum.getPrecursors()[0].getMZ();
90  Size j = 0;
91  for (Size i = 0; i < bands; ++i)
92  {
93  double intensity = 0;
94 
95  //bern 2004 says to only check between 300 and size
96  //but that seems inappropriate for small peptides (smallest is ca 450)
97  while (j < spectrum.size() && spectrum[j].getPosition()[0] < (parentmass - 300) / bands * (i + 1) + 300)
98  {
99  intensity += spectrum[j++].getIntensity();
100  }
101  band_intensity.insert(std::make_pair(intensity, i));
102  }
103  j = 0;
104  double total_intensity = 0;
105  double twobiggest = 0;
106  double sevensmallest = 0;
107  for (std::multimap<double, Size>::reverse_iterator mmrit = band_intensity.rbegin(); mmrit != band_intensity.rend(); ++mmrit, ++j)
108  {
109  total_intensity += mmrit->first;
110  //take the two biggest
111  if (j < 2)
112  {
113  twobiggest += mmrit->first;
114  }
115  //take the seven smallest
116  if (j > 2)
117  {
118  sevensmallest += mmrit->first;
119  }
120  }
121 
122  return (twobiggest - sevensmallest) / total_intensity;
123  }
124 
126  static const String getProductName()
127  {
128  return "IntensityBalanceFilter";
129  }
130 
131  // @}
132 
133  };
134 }
135 #endif // OPENMS_FILTERING_TRANSFORMERS_INTENSITYBALANCEFILTER_H
A more convenient string class.
Definition: String.h:57
double apply(SpectrumType &spectrum)
Definition: IntensityBalanceFilter.h:84
static FilterFunctor * create()
Definition: IntensityBalanceFilter.h:80
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
static const String getProductName()
Definition: IntensityBalanceFilter.h:126
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
A FilterFunctor extracts some spectrum characteristics for quality assessment.
Definition: FilterFunctor.h:45
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
IntensityBalanceFilter divides the m/z-range into ten regions and sums the intensity in these regions...
Definition: IntensityBalanceFilter.h:53
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:01 using doxygen 1.8.13