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ComplementMarker.h
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35 #ifndef OPENMS_FILTERING_TRANSFORMERS_COMPLEMENTMARKER_H
36 #define OPENMS_FILTERING_TRANSFORMERS_COMPLEMENTMARKER_H
37 
39 
40 #include <map>
41 #include <cmath>
42 
43 namespace OpenMS
44 {
52  class OPENMS_DLLAPI ComplementMarker :
53  public PeakMarker
54  {
55 public:
56 
57  // @name Constructors and Destructors
61 
63  ComplementMarker(const ComplementMarker & source);
64 
66  virtual ~ComplementMarker();
68 
69  // @name Operators
71  ComplementMarker & operator=(const ComplementMarker & source);
74 
75  // @name Accessors
77  static PeakMarker * create() { return new ComplementMarker(); }
79 
81  template <typename SpectrumType>
82  void apply(std::map<double, bool> marked, SpectrumType & spectrum)
83  {
84  if (spectrum.size() < 2)
85  {
86  return;
87  }
88 
89  // how often a peak needs to be marked to be returned
90  double marks = (double)param_.getValue("marks");
91  double parentmass = 0.0;
92  if (!spectrum.getPrecursors().empty()) parentmass = spectrum.getPrecursors()[0].getMZ();
93  double tolerance = (double)param_.getValue("tolerance");
94  std::map<double, int> matching_b_y_ions;
95 
96  spectrum.sortByPosition();
97 
98  SignedSize j = spectrum.size() - 1;
99  for (Size i = 0; i < spectrum.size(); ++i)
100  {
101  while (j >= 0 && spectrum[j].getPosition()[0] > (parentmass - spectrum[i].getPosition()[0]) + tolerance)
102  {
103  j--;
104  }
105 
106  // just takes the first matching ion; todo take all
107  if (j >= 0 && std::fabs(spectrum[i].getPosition()[0] + spectrum[j].getPosition()[0] - parentmass) < tolerance)
108  {
109  matching_b_y_ions[spectrum[i].getPosition()[0]]++;
110  matching_b_y_ions[spectrum[j].getPosition()[0]]++;
111  j--;
112  }
113  }
114 
115  for (std::map<double, int>::const_iterator cmit = matching_b_y_ions.begin(); cmit != matching_b_y_ions.end(); ++cmit)
116  {
117  if (cmit->second >= marks)
118  {
119  marked.insert(std::pair<double, bool>(cmit->first, true));
120  }
121  }
122  }
123 
125  static const String getProductName()
126  {
127  return "ComplementMarker";
128  }
129 
131 
132  };
133 
134 }
135 #endif //OPENMS_FILTERING_TRANSFORMERS_COMPLEMENTMARKER_H
ComplementMarker marks peak pairs which could represent y - b ion pairs.
Definition: ComplementMarker.h:52
A more convenient string class.
Definition: String.h:57
void sortByPosition()
Lexicographically sorts the peaks by their position.
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:135
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
PeakMarker marks peaks that seem to fulfill some criterion.
Definition: PeakMarker.h:48
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
void apply(std::map< double, bool > marked, SpectrumType &spectrum)
Definition: ComplementMarker.h:82
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
static const String getProductName()
returns the name to register at the factory
Definition: ComplementMarker.h:125

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:21:59 using doxygen 1.8.13