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IMSIsotopeDistribution.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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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: Timo Sachsenberg $
32 // $Authors: Anton Pervukhin <Anton.Pervukhin@CeBiTec.Uni-Bielefeld.DE> $
33 // --------------------------------------------------------------------------
34 //
35
36 #pragma once
37
38 #include <vector>
39 #include <ostream>
40 #include <algorithm>
41
42 #include <OpenMS/config.h>
43
44 namespace OpenMS
45 {
46
47 namespace ims
48 {
49
87 class OPENMS_DLLAPI IMSIsotopeDistribution
88 {
89
90 public:
92 typedef double mass_type;
93
95 typedef double abundance_type;
96
98 typedef unsigned int nominal_mass_type;
99
101 struct Peak
102 {
103 Peak(mass_type local_mass = 0.0, abundance_type local_abundance = 0.0) :
104 mass(local_mass), abundance(local_abundance)
105 {}
106
107 bool operator==(const Peak & peak) const
108 {
109 #pragma clang diagnostic push
110 #pragma clang diagnostic ignored "-Wfloat-equal"
111 return peak.mass == mass && peak.abundance == abundance;
112 #pragma clang diagnostic pop
113 }
114
115 mass_type mass;
116 abundance_type abundance;
117 };
118
120 typedef Peak peak_type;
121
123 typedef std::vector<peak_type> peaks_container;
124
126 typedef peaks_container::iterator peaks_iterator;
127
129 typedef peaks_container::const_iterator const_peaks_iterator;
130
132 typedef peaks_container::size_type size_type;
133
135 typedef std::vector<mass_type> masses_container;
136
138 typedef masses_container::iterator masses_iterator;
139
141 typedef masses_container::const_iterator const_masses_iterator;
142
144 typedef std::vector<abundance_type> abundances_container;
145
147 typedef abundances_container::iterator abundances_iterator;
148
150 typedef abundances_container::const_iterator const_abundances_iterator;
151
153 static abundance_type ABUNDANCES_SUM_ERROR;
154
156 static size_type SIZE;
157
159 explicit IMSIsotopeDistribution(nominal_mass_type nominalMass = 0) :
160 nominal_mass_(nominalMass)
161 {}
162
164 explicit IMSIsotopeDistribution(mass_type mass) :
165 nominal_mass_(0)
166 {
167 peaks_.push_back(peaks_container::value_type(mass, 1.0));
168 }
169
171 IMSIsotopeDistribution(const peaks_container & peaks,
172 nominal_mass_type nominalMass = 0) :
173 peaks_(peaks),
174 nominal_mass_(nominalMass)
175 {}
176
178 IMSIsotopeDistribution(const IMSIsotopeDistribution & distribution) :
179 peaks_(distribution.peaks_),
180 nominal_mass_(distribution.nominal_mass_)
181 {}
182
184 ~IMSIsotopeDistribution()
185 {}
186
193 size_type size() const { return std::min(peaks_.size(), SIZE); }
194
201 IMSIsotopeDistribution & operator=(
202 const IMSIsotopeDistribution & distribution);
203
211 bool operator==(const IMSIsotopeDistribution & distribution) const;
212
220 bool operator!=(const IMSIsotopeDistribution & distribution) const;
221
232 IMSIsotopeDistribution & operator*=(
233 const IMSIsotopeDistribution & distribution);
234
245 IMSIsotopeDistribution & operator*=(unsigned int pow);
246
253 mass_type getMass(size_type i) const
254 {
255 return peaks_[i].mass + nominal_mass_ + i;
256 }
257
264 abundance_type getAbundance(size_type i) const
265 {
266 return peaks_[i].abundance;
267 }
268
274 mass_type getAverageMass() const;
275
281 nominal_mass_type getNominalMass() const { return nominal_mass_; }
282
288 void setNominalMass(nominal_mass_type nominalMass)
289 {
290 this->nominal_mass_ = nominalMass;
291 }
292
298 masses_container getMasses() const;
299
305 abundances_container getAbundances() const;
306
312 void normalize();
313
319 bool empty() const { return peaks_.empty(); }
320
321 private:
323 peaks_container peaks_;
324
326 nominal_mass_type nominal_mass_;
327
329 void setMinimumSize_();
330 };
331
338 OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os,
339 const IMSIsotopeDistribution & distribution);
340
341 } // namespace ims
342 } // namespace OpenMS
343
OpenMS::ims::IMSIsotopeDistribution::peaks_iterator
peaks_container::iterator peaks_iterator
Type of iterator over container with peaks.
Definition: IMSIsotopeDistribution.h:126
OpenMS::ims::IMSIsotopeDistribution::abundances_container
std::vector< abundance_type > abundances_container
Type of container with isotope abundances.
Definition: IMSIsotopeDistribution.h:144
OpenMS::ims::IMSIsotopeDistribution::IMSIsotopeDistribution
IMSIsotopeDistribution(nominal_mass_type nominalMass=0)
Constructor with nominal mass.
Definition: IMSIsotopeDistribution.h:159
OpenMS::ims::operator<<
std::ostream & operator<<(std::ostream &os, const IMSAlphabet &alphabet)
OpenMS::ims::IMSIsotopeDistribution::setNominalMass
void setNominalMass(nominal_mass_type nominalMass)
Definition: IMSIsotopeDistribution.h:288
OpenMS::ims::IMSIsotopeDistribution::size_type
peaks_container::size_type size_type
Type of peaks container&#39;s size.
Definition: IMSIsotopeDistribution.h:132
OpenMS::ims::IMSIsotopeDistribution::Peak
Structure that represents an isotope peak - pair of mass and abundance.
Definition: IMSIsotopeDistribution.h:101
OpenMS::ims::IMSIsotopeDistribution::Peak::abundance
abundance_type abundance
Definition: IMSIsotopeDistribution.h:116
OpenMS::ims::IMSIsotopeDistribution::Peak::operator==
bool operator==(const Peak &peak) const
Definition: IMSIsotopeDistribution.h:107
OpenMS::ims::IMSIsotopeDistribution::peaks_container
std::vector< peak_type > peaks_container
Type of container to store peaks.
Definition: IMSIsotopeDistribution.h:123
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::ims::IMSIsotopeDistribution::nominal_mass_
nominal_mass_type nominal_mass_
Nominal mass of distribution.
Definition: IMSIsotopeDistribution.h:326
OpenMS::ims::IMSIsotopeDistribution::abundance_type
double abundance_type
Type of isotope abundance.
Definition: IMSIsotopeDistribution.h:95
OpenMS::ims::IMSIsotopeDistribution::peak_type
Peak peak_type
Type of isotope peak.
Definition: IMSIsotopeDistribution.h:120
OpenMS::ims::IMSIsotopeDistribution::peaks_
peaks_container peaks_
Container for isotopes.
Definition: IMSIsotopeDistribution.h:323
OpenMS::ims::IMSIsotopeDistribution::Peak::mass
mass_type mass
Definition: IMSIsotopeDistribution.h:115
OpenMS::ims::IMSIsotopeDistribution::size
size_type size() const
Definition: IMSIsotopeDistribution.h:193
OpenMS::ims::IMSIsotopeDistribution
Represents a distribution of isotopes restricted to the first K elements.
Definition: IMSIsotopeDistribution.h:87
OpenMS::ims::IMSIsotopeDistribution::const_peaks_iterator
peaks_container::const_iterator const_peaks_iterator
Type of const iterator over container with peaks.
Definition: IMSIsotopeDistribution.h:129
OpenMS::ims::IMSIsotopeDistribution::IMSIsotopeDistribution
IMSIsotopeDistribution(mass_type mass)
Constructor with single isotope.
Definition: IMSIsotopeDistribution.h:164
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ims::IMSIsotopeDistribution::masses_iterator
masses_container::iterator masses_iterator
Type of iterator over container with isotope masses.
Definition: IMSIsotopeDistribution.h:138
OpenSwath::normalize
OPENSWATHALGO_DLLAPI void normalize(const std::vector< double > &intensities, double normalization_factor, std::vector< double > &normalized_intensities)
Normalize intensities in vector by normalization_factor.
OpenMS::ims::IMSIsotopeDistribution::const_abundances_iterator
abundances_container::const_iterator const_abundances_iterator
Type of const iterator over container with isotope abundances.
Definition: IMSIsotopeDistribution.h:150
OpenMS::ims::IMSIsotopeDistribution::IMSIsotopeDistribution
IMSIsotopeDistribution(const IMSIsotopeDistribution &distribution)
Copy constructor.
Definition: IMSIsotopeDistribution.h:178
double
OpenMS::ims::IMSIsotopeDistribution::getAbundance
abundance_type getAbundance(size_type i) const
Definition: IMSIsotopeDistribution.h:264
OpenMS::ims::IMSIsotopeDistribution::ABUNDANCES_SUM_ERROR
static abundance_type ABUNDANCES_SUM_ERROR
Error to be allowed for isotope distribution.
Definition: IMSIsotopeDistribution.h:153
OpenMS::ims::IMSIsotopeDistribution::masses_container
std::vector< mass_type > masses_container
Type of container with isotope masses.
Definition: IMSIsotopeDistribution.h:135
OpenMS::ims::IMSIsotopeDistribution::IMSIsotopeDistribution
IMSIsotopeDistribution(const peaks_container &peaks, nominal_mass_type nominalMass=0)
Constructor with isotopes and nominal mass.
Definition: IMSIsotopeDistribution.h:171
OpenMS::ims::IMSIsotopeDistribution::abundances_iterator
abundances_container::iterator abundances_iterator
Type of iterator over container with isotope abundances.
Definition: IMSIsotopeDistribution.h:147
OpenMS::ims::IMSIsotopeDistribution::mass_type
double mass_type
Type of isotope mass.
Definition: IMSIsotopeDistribution.h:92
OpenMS::ims::IMSIsotopeDistribution::const_masses_iterator
masses_container::const_iterator const_masses_iterator
Type of const iterator over container with isotope masses.
Definition: IMSIsotopeDistribution.h:141
OpenMS::ims::IMSIsotopeDistribution::empty
bool empty() const
Definition: IMSIsotopeDistribution.h:319
OpenMS::ims::IMSIsotopeDistribution::getNominalMass
nominal_mass_type getNominalMass() const
Definition: IMSIsotopeDistribution.h:281
OpenMS::ims::IMSIsotopeDistribution::getMass
mass_type getMass(size_type i) const
Definition: IMSIsotopeDistribution.h:253
OpenMS::ims::IMSIsotopeDistribution::Peak::Peak
Peak(mass_type local_mass=0.0, abundance_type local_abundance=0.0)
Definition: IMSIsotopeDistribution.h:103
OpenMS::ims::IMSIsotopeDistribution::nominal_mass_type
unsigned int nominal_mass_type
Type of isotope nominal mass.
Definition: IMSIsotopeDistribution.h:98
OpenMS::ims::IMSIsotopeDistribution::~IMSIsotopeDistribution
~IMSIsotopeDistribution()
Destructor.
Definition: IMSIsotopeDistribution.h:184
OpenMS::ims::IMSIsotopeDistribution::SIZE
static size_type SIZE
Length of isotope distribution.
Definition: IMSIsotopeDistribution.h:156
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806