OpenMS  3.0.0
NeutralLossMarker.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 NeutralLossMarker :
52  public PeakMarker
53  {
54 public:
55 
56  // @name Constructors and Destructors
57  // @{
60 
62  NeutralLossMarker(const NeutralLossMarker & source);
63 
65  ~NeutralLossMarker() override;
66  // @}
67 
68  // @name Operators
69  // @{
71  NeutralLossMarker & operator=(const NeutralLossMarker & source);
72  // @}
73 
74  // @name Accessors
75  // @{
77  static PeakMarker * create() { return new NeutralLossMarker(); }
78 
80  template <typename SpectrumType>
81  void apply(std::map<double, bool> & marked, SpectrumType & spectrum)
82  {
83  // how often a peak needs to be marked to be returned
84  double marks = (double)param_.getValue("marks");
85  double tolerance = (double)param_.getValue("tolerance");
86  std::map<double, SignedSize> ions_w_neutrallosses;
87  spectrum.sortByPosition();
88  for (Size i = 0; i < spectrum.size(); ++i)
89  {
90  double mz = spectrum[i].getPosition()[0];
91  double intensity = spectrum[i].getIntensity();
92  SignedSize j = i - 1;
93  while (j >= 0)
94  {
95  double curmz = spectrum[j].getPosition()[0];
96  double curIntensity = spectrum[j].getIntensity();
97 
98  // check for peak that's a water or ammonia away
99  if (std::fabs(mz - curmz - 17) < tolerance || std::fabs(mz - curmz - 18) < tolerance)
100  {
101  // neutral loss peak should be smaller
102  if (curIntensity < intensity)
103  {
104  ions_w_neutrallosses[mz]++;
105  // neutral loss peak not marked
106  //ions_w_neutrallosses[curmz]++;
107  }
108  }
109  else
110  {
111  if (mz - curmz > 18.3)
112  {
113  break;
114  }
115  }
116  --j;
117  }
118  }
119 
120  for (std::map<double, SignedSize>::const_iterator cmit = ions_w_neutrallosses.begin(); cmit != ions_w_neutrallosses.end(); ++cmit)
121  {
122  if (cmit->second >= marks)
123  {
124  marked.insert(std::pair<double, bool>(cmit->first, true));
125  }
126  }
127  return;
128  }
129 
131  static const String getProductName()
132  {
133  return "NeutralLossMarker";
134  }
135 
136  // @}
137 
138  };
139 
140 }
double
PeakMarker.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::NeutralLossMarker
NeutralLossMarker marks peak pairs which could represent an ion an its neutral loss (water,...
Definition: NeutralLossMarker.h:51
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::NeutralLossMarker::getProductName
static const String getProductName()
Definition: NeutralLossMarker.h:131
OpenMS::NeutralLossMarker::create
static PeakMarker * create()
Definition: NeutralLossMarker.h:77
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::NeutralLossMarker::apply
void apply(std::map< double, bool > &marked, SpectrumType &spectrum)
Definition: NeutralLossMarker.h:81
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