| OpenMS 2.5.0

IsotopeDistribution.h
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2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Chris Bielow $
32 // $Authors: Clemens Groepl, Andreas Bertsch, Chris Bielow $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/Peak1D.h>
38
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
90 IsotopeDistribution();
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
226 protected:
227
229 void sort_(std::function<bool(const MassAbundance& p1, const MassAbundance& p2)> sorter);
230
232 void transform_(std::function<void(MassAbundance&)> lambda);
233
235 ContainerType distribution_;
236 };
237
238
239 } // namespace OpenMS
240
OpenMS::IsotopeDistribution::distribution_
ContainerType distribution_
stores the isotope distribution
Definition: IsotopeDistribution.h:235
OpenMS::IsotopeDistribution::rend
ConstReverseIterator rend() const
Definition: IsotopeDistribution.h:212
OpenMS::IsotopeDistribution::end
Iterator end()
Definition: IsotopeDistribution.h:200
OpenMS::IsotopeDistribution::begin
Iterator begin()
Definition: IsotopeDistribution.h:198
OpenMS::IsotopeDistribution::ConstReverseIterator
ContainerType::const_reverse_iterator ConstReverseIterator
Definition: IsotopeDistribution.h:81
OpenMS::IsotopeDistribution::rend
ReverseIterator rend()
Definition: IsotopeDistribution.h:208
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:64
OpenMS::IsotopeDistribution::Sorted
Sorted
Definition: IsotopeDistribution.h:84
OpenMS::IsotopeDistribution::end
ConstIterator end() const
Definition: IsotopeDistribution.h:204
OpenMS::IsotopeDistribution::iterator
ContainerType::iterator iterator
Definition: IsotopeDistribution.h:73
Peak1D.h
OpenMS::IsotopeDistribution::Iterator
ContainerType::iterator Iterator
Definition: IsotopeDistribution.h:74
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::IsotopeDistribution::const_iterator
ContainerType::const_iterator const_iterator
Definition: IsotopeDistribution.h:75
OpenMS::IsotopeDistribution::const_reverse_iterator
ContainerType::const_reverse_iterator const_reverse_iterator
Definition: IsotopeDistribution.h:80
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::IsotopeDistribution::rbegin
ConstReverseIterator rbegin() const
Definition: IsotopeDistribution.h:210
OpenMS::IsotopeDistribution::rbegin
ReverseIterator rbegin()
Definition: IsotopeDistribution.h:206
OpenMS::IsotopeDistribution::ConstIterator
ContainerType::const_iterator ConstIterator
Definition: IsotopeDistribution.h:76
double
float
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::IsotopeDistribution::ReverseIterator
ContainerType::reverse_iterator ReverseIterator
Definition: IsotopeDistribution.h:79
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::IsotopeDistribution::reverse_iterator
ContainerType::reverse_iterator reverse_iterator
Definition: IsotopeDistribution.h:78
OpenMS::IsotopeDistribution::ContainerType
std::vector< MassAbundance > ContainerType
Definition: IsotopeDistribution.h:72