OpenMS  3.0.0
IsotopeDistribution.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Clemens Groepl, Andreas Bertsch, Chris Bielow $
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34 
35 #pragma once
36 
37 #include <OpenMS/KERNEL/Peak1D.h>
38 #include <functional>
39 #include <vector>
40 
41 namespace OpenMS
42 {
62  class Element;
63 
64  class OPENMS_DLLAPI IsotopeDistribution
65  {
66 public:
67 
69 
70  typedef Peak1D MassAbundance;
72  typedef std::vector<MassAbundance> ContainerType;
73  typedef ContainerType::iterator iterator;
74  typedef ContainerType::iterator Iterator;
75  typedef ContainerType::const_iterator const_iterator;
76  typedef ContainerType::const_iterator ConstIterator;
77 
78  typedef ContainerType::reverse_iterator reverse_iterator;
79  typedef ContainerType::reverse_iterator ReverseIterator;
80  typedef ContainerType::const_reverse_iterator const_reverse_iterator;
81  typedef ContainerType::const_reverse_iterator ConstReverseIterator;
83 
84  enum Sorted {INTENSITY, MASS, UNDEFINED};
85 
87 
88 
91 
93  IsotopeDistribution(const IsotopeDistribution&) = default;
94 
96  IsotopeDistribution(IsotopeDistribution&&) noexcept = default;
97 
99  virtual ~IsotopeDistribution() = default;
101 
103 
104 
106  void set(const ContainerType & distribution);
107 
109  void set(ContainerType && distribution);
110 
112  const ContainerType & getContainer() const;
113 
115  Peak1D::CoordinateType getMax() const;
116 
118  Peak1D::CoordinateType getMin() const;
119 
121  Peak1D getMostAbundant() const;
122 
124  Size size() const;
125 
127  void clear();
128 
129  // resizes distribution container
130  void resize(UInt size);
131 
133  void trimIntensities(double cutoff);
134 
136  void sortByIntensity();
137 
139  void sortByMass();
140 
146  void renormalize();
147 
155  void merge(double resolution, double min_prob);
156 
165  void trimRight(double cutoff);
166 
175  void trimLeft(double cutoff);
176 
178  double averageMass() const;
180 
182 
183  IsotopeDistribution & operator=(const IsotopeDistribution & isotope_distribution);
185 
187  bool operator==(const IsotopeDistribution & isotope_distribution) const;
188 
190  bool operator!=(const IsotopeDistribution & isotope_distribution) const;
191 
193  bool operator<(const IsotopeDistribution & isotope_distribution) const;
195 
197 
198  inline Iterator begin() { return distribution_.begin(); }
199 
200  inline Iterator end() { return distribution_.end(); }
201 
202  inline ConstIterator begin() const { return distribution_.begin(); }
203 
204  inline ConstIterator end() const { return distribution_.end(); }
205 
206  inline ReverseIterator rbegin() { return distribution_.rbegin(); }
207 
208  inline ReverseIterator rend() { return distribution_.rend(); }
209 
210  inline ConstReverseIterator rbegin() const { return distribution_.rbegin(); }
211 
212  inline ConstReverseIterator rend() const { return distribution_.rend(); }
213 
214  inline void insert(const Peak1D::CoordinateType& mass, const Peak1D::IntensityType& intensity)
215  {
216  distribution_.push_back(Peak1D(mass, intensity));
217  }
219 
221 
222  Peak1D& operator[](const Size& index){ return distribution_[index];}
225  const Peak1D& operator[](const Size& index) const { return distribution_[index]; }
227 
228 protected:
229 
231  void sort_(std::function<bool(const MassAbundance& p1, const MassAbundance& p2)> sorter);
232 
234  void transform_(std::function<void(MassAbundance&)> lambda);
235 
238  };
239 
240 
241 } // namespace OpenMS
242 
OpenMS::IsotopeDistribution::Iterator
ContainerType::iterator Iterator
Definition: IsotopeDistribution.h:74
OpenMS::IsotopeDistribution::ContainerType
std::vector< MassAbundance > ContainerType
Definition: IsotopeDistribution.h:72
OpenMS::IsotopeDistribution::reverse_iterator
ContainerType::reverse_iterator reverse_iterator
Definition: IsotopeDistribution.h:78
OpenMS::IsotopeDistribution::rend
ReverseIterator rend()
Definition: IsotopeDistribution.h:208
OpenMS::IsotopeDistribution::ReverseIterator
ContainerType::reverse_iterator ReverseIterator
Definition: IsotopeDistribution.h:79
double
OpenMS::IsotopeDistribution::distribution_
ContainerType distribution_
stores the isotope distribution
Definition: IsotopeDistribution.h:237
OpenMS::IsotopeDistribution::end
Iterator end()
Definition: IsotopeDistribution.h:200
OpenMS::IsotopeDistribution::operator[]
const Peak1D & operator[](const Size &index) const
const operator to access a cell of the distribution and wraps it in SpectrumFragment struct
Definition: IsotopeDistribution.h:225
Peak1D.h
OpenMS::IsotopeDistribution::const_reverse_iterator
ContainerType::const_reverse_iterator const_reverse_iterator
Definition: IsotopeDistribution.h:80
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::IsotopeDistribution::ConstIterator
ContainerType::const_iterator ConstIterator
Definition: IsotopeDistribution.h:76
OpenMS::IsotopeDistribution::begin
Iterator begin()
Definition: IsotopeDistribution.h:198
OpenMS::IsotopeDistribution::rbegin
ReverseIterator rbegin()
Definition: IsotopeDistribution.h:206
OpenMS::IsotopeDistribution::ConstReverseIterator
ContainerType::const_reverse_iterator ConstReverseIterator
Definition: IsotopeDistribution.h:81
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::IsotopeDistribution::rend
ConstReverseIterator rend() const
Definition: IsotopeDistribution.h:212
OpenMS::IsotopeDistribution::begin
ConstIterator begin() const
Definition: IsotopeDistribution.h:202
OpenMS::IsotopeDistribution::insert
void insert(const Peak1D::CoordinateType &mass, const Peak1D::IntensityType &intensity)
Definition: IsotopeDistribution.h:214
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:53
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:64
OpenMS::IsotopeDistribution::end
ConstIterator end() const
Definition: IsotopeDistribution.h:204
float
OpenMS::IsotopeDistribution::Sorted
Sorted
Definition: IsotopeDistribution.h:84
OpenMS::IsotopeDistribution::const_iterator
ContainerType::const_iterator const_iterator
Definition: IsotopeDistribution.h:75
OpenMS::IsotopeDistribution::rbegin
ConstReverseIterator rbegin() const
Definition: IsotopeDistribution.h:210
OpenMS::IsotopeDistribution::iterator
ContainerType::iterator iterator
Definition: IsotopeDistribution.h:73