OpenMS  3.0.0
ComplementMarker.h
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31 // $Maintainer: Timo Sachsenberg $
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34 //
35 #pragma once
36 
38 
39 #include <map>
40 #include <cmath>
41 
42 namespace OpenMS
43 {
51  class OPENMS_DLLAPI ComplementMarker :
52  public PeakMarker
53  {
54 public:
55 
56  // @name Constructors and Destructors
60 
62  ComplementMarker(const ComplementMarker & source);
63 
65  ~ComplementMarker() override;
67 
68  // @name Operators
70  ComplementMarker & operator=(const ComplementMarker & source);
73 
74  // @name Accessors
76  static PeakMarker * create() { return new ComplementMarker(); }
78 
80  template <typename SpectrumType>
81  void apply(std::map<double, bool> marked, SpectrumType & spectrum)
82  {
83  if (spectrum.size() < 2)
84  {
85  return;
86  }
87 
88  // how often a peak needs to be marked to be returned
89  double marks = (double)param_.getValue("marks");
90  double parentmass = 0.0;
91  if (!spectrum.getPrecursors().empty()) parentmass = spectrum.getPrecursors()[0].getMZ();
92  double tolerance = (double)param_.getValue("tolerance");
93  std::map<double, int> matching_b_y_ions;
94 
95  spectrum.sortByPosition();
96 
97  SignedSize j = spectrum.size() - 1;
98  for (Size i = 0; i < spectrum.size(); ++i)
99  {
100  while (j >= 0 && spectrum[j].getPosition()[0] > (parentmass - spectrum[i].getPosition()[0]) + tolerance)
101  {
102  j--;
103  }
104 
105  // just takes the first matching ion; todo take all
106  if (j >= 0 && std::fabs(spectrum[i].getPosition()[0] + spectrum[j].getPosition()[0] - parentmass) < tolerance)
107  {
108  matching_b_y_ions[spectrum[i].getPosition()[0]]++;
109  matching_b_y_ions[spectrum[j].getPosition()[0]]++;
110  j--;
111  }
112  }
113 
114  for (std::map<double, int>::const_iterator cmit = matching_b_y_ions.begin(); cmit != matching_b_y_ions.end(); ++cmit)
115  {
116  if (cmit->second >= marks)
117  {
118  marked.insert(std::pair<double, bool>(cmit->first, true));
119  }
120  }
121  }
122 
124  static const String getProductName()
125  {
126  return "ComplementMarker";
127  }
128 
130 
131  };
132 
133 }
double
OpenMS::ComplementMarker::apply
void apply(std::map< double, bool > marked, SpectrumType &spectrum)
Definition: ComplementMarker.h:81
PeakMarker.h
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
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ComplementMarker
ComplementMarker marks peak pairs which could represent y - b ion pairs.
Definition: ComplementMarker.h:51
OpenMS::ComplementMarker::getProductName
static const String getProductName()
returns the name to register at the factory
Definition: ComplementMarker.h:124
OpenMS::MSSpectrum::sortByPosition
void sortByPosition()
Lexicographically sorts the peaks by their position.
OpenMS::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
OpenMS::PeakMarker
PeakMarker marks peaks that seem to fulfill some criterion.
Definition: PeakMarker.h:47
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66