| OpenMS 2.5.0

IntensityBalanceFilter.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 //
35 #pragma once
36
37 #include <OpenMS/FILTERING/TRANSFORMERS/FilterFunctor.h>
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 // @{
61 IntensityBalanceFilter();
62
64 IntensityBalanceFilter(const IntensityBalanceFilter & source);
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::IntensityBalanceFilter::create
static FilterFunctor * create()
Definition: IntensityBalanceFilter.h:79
OpenMS::SpectrumSettings::getPrecursors
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
OpenMS::IntensityBalanceFilter::getProductName
static const String getProductName()
Definition: IntensityBalanceFilter.h:125
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::FilterFunctor
A FilterFunctor extracts some spectrum characteristics for quality assessment.
Definition: FilterFunctor.h:44
OpenMS::IntensityBalanceFilter
IntensityBalanceFilter divides the m/z-range into ten regions and sums the intensity in these regions...
Definition: IntensityBalanceFilter.h:52
OpenMS::IntensityBalanceFilter::apply
double apply(SpectrumType &spectrum)
Definition: IntensityBalanceFilter.h:83
FilterFunctor.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127