OpenMS  3.0.0
BinnedSpectrum.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg, Mathias Walzer $
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34 //
35 #pragma once
36 
40 
41 #include <cmath>
42 
43 // forward decl
44 namespace Eigen
45 {
46  template<typename _Scalar, int _Flags, typename _StorageIndex>
47  class SparseVector;
48 }
49 
50 namespace OpenMS
51 {
52 
80  class OPENMS_DLLAPI BinnedSpectrum
81  {
82  // smallest possible m/z value (needs to be >= 1)
83  static constexpr const float MIN_MZ_ = 1.0;
84 
85 public:
100  // default bin width for low-resolution data (adapted from doi:10.1007/s13361-015-1179-x)
101  static constexpr const float DEFAULT_BIN_WIDTH_LOWRES = 1.0005f;
102 
103  // default bin width for high-resolution data (adapted from doi:10.1007/s13361-015-1179-x)
104  static constexpr const float DEFAULT_BIN_WIDTH_HIRES = 0.02f;
105 
107  static constexpr const float DEFAULT_BIN_OFFSET_HIRES = 0.0f;
108 
110  static constexpr const float DEFAULT_BIN_OFFSET_LOWRES = 0.4f;
111 
114 
116  // static const SparseVectorType EmptySparseVector;
117 
119  // BinnedSpectrum() = delete;
121 
123  BinnedSpectrum(const PeakSpectrum& ps, float size, bool unit_ppm, UInt spread, float offset);
124 
127 
129  virtual ~BinnedSpectrum();
130 
132  BinnedSpectrum& operator=(const BinnedSpectrum&);
133 
135  bool operator==(const BinnedSpectrum& rhs) const;
136 
138  bool operator!=(const BinnedSpectrum& rhs) const;
139 
141  float getBinIntensity(double mz);
142 
144  size_t getBinIndex(float mz) const;
145 
147  inline float getBinLowerMZ(size_t i) const
148  {
149  if (unit_ppm_)
150  {
151  // mz = MIN_MZ_ * (1.0 + bin_size_)^index for index
152  return (MIN_MZ_ * pow(1.0 + bin_size_ * 1e-6, i));
153  }
154  else
155  {
156  return ((static_cast<float>(i) - offset_) * bin_size_);
157  }
158  }
159 
161  inline float getBinSize() const { return bin_size_; }
162 
164  inline size_t getBinSpread() const { return bin_spread_; }
165 
167  const SparseVectorType* getBins() const;
168 
170  SparseVectorType* getBins();
171 
173  inline float getOffset() const { return offset_; }
174 
176  const std::vector<Precursor>& getPrecursors() const;
177 
179  std::vector<Precursor>& getPrecursors();
180 
182  // returns true if bin size, unit and offset are equal, otherwise false
183  static bool isCompatible(const BinnedSpectrum& a, const BinnedSpectrum& b);
184 
185 private:
188 
190  float bin_size_;
191 
193  bool unit_ppm_;
194 
196  float offset_;
197 
200 
202  void binSpectrum_(const PeakSpectrum& ps);
203 
205  std::vector<Precursor> precursors_;
206  };
207 
208 }
209 
OpenMS::BinnedSpectrum::getBinSize
float getBinSize() const
get the bin size
Definition: BinnedSpectrum.h:161
Eigen
Definition: IsobaricIsotopeCorrector.h:40
OpenMS::BinnedSpectrum::bin_spread_
UInt bin_spread_
the spread to left or right
Definition: BinnedSpectrum.h:187
OpenMS::BinnedSpectrum::BinnedSpectrum
BinnedSpectrum()
the empty SparseVector
Definition: BinnedSpectrum.h:120
OpenMS::BinnedSpectrum
This is a binned representation of a PeakSpectrum.
Definition: BinnedSpectrum.h:80
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::BinnedSpectrum::precursors_
std::vector< Precursor > precursors_
precursor information
Definition: BinnedSpectrum.h:205
OpenMS::BinnedSpectrum::unit_ppm_
bool unit_ppm_
absolute bin size or relative bin size
Definition: BinnedSpectrum.h:193
OpenMS::BinnedSpectrum::getBinLowerMZ
float getBinLowerMZ(size_t i) const
return the lower m/z of a bin given its index
Definition: BinnedSpectrum.h:147
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::BinnedSpectrum::bins_
SparseVectorType * bins_
bins
Definition: BinnedSpectrum.h:199
Exception.h
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::BinnedSpectrum::bin_size_
float bin_size_
the size of each bin
Definition: BinnedSpectrum.h:190
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
Eigen::SparseVector
Definition: BinnedSpectrum.h:47
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
StandardTypes.h
MSSpectrum.h
OpenMS::BinnedSpectrum::offset_
float offset_
offset of bin start
Definition: BinnedSpectrum.h:196
OpenMS::BinnedSpectrum::getBinSpread
size_t getBinSpread() const
get the bin spread
Definition: BinnedSpectrum.h:164
OpenMS::BinnedSpectrum::getOffset
float getOffset() const
return offset
Definition: BinnedSpectrum.h:173