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IMSIsotopeDistribution.h
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35 
36 #ifndef OPENMS_CHEMISTRY_MASSDECOMPOSITION_IMS_IMSISOTOPEDISTRIBUTION_H
37 #define OPENMS_CHEMISTRY_MASSDECOMPOSITION_IMS_IMSISOTOPEDISTRIBUTION_H
38 
39 #include <vector>
40 #include <ostream>
41 #include <algorithm>
42 
43 #include <OpenMS/config.h>
44 
45 namespace OpenMS
46 {
47 
48  namespace ims
49  {
50 
88  class OPENMS_DLLAPI IMSIsotopeDistribution
89  {
90 
91 public:
93  typedef double mass_type;
94 
96  typedef double abundance_type;
97 
99  typedef unsigned int nominal_mass_type;
100 
102  struct Peak
103  {
104  Peak(mass_type mass = 0.0, abundance_type abundance = 0.0) :
105  mass(mass), abundance(abundance)
106  {}
107 
108  bool operator==(const Peak & peak) const
109  {
110  return peak.mass == mass && peak.abundance == abundance;
111  }
112 
115  };
116 
118  typedef Peak peak_type;
119 
121  typedef std::vector<peak_type> peaks_container;
122 
124  typedef peaks_container::iterator peaks_iterator;
125 
127  typedef peaks_container::const_iterator const_peaks_iterator;
128 
130  typedef peaks_container::size_type size_type;
131 
133  typedef std::vector<mass_type> masses_container;
134 
136  typedef masses_container::iterator masses_iterator;
137 
139  typedef masses_container::const_iterator const_masses_iterator;
140 
142  typedef std::vector<abundance_type> abundances_container;
143 
145  typedef abundances_container::iterator abundances_iterator;
146 
148  typedef abundances_container::const_iterator const_abundances_iterator;
149 
152 
154  static size_type SIZE;
155 
157  explicit IMSIsotopeDistribution(nominal_mass_type nominalMass = 0) :
158  nominal_mass_(nominalMass)
159  {}
160 
163  nominal_mass_(0)
164  {
165  peaks_.push_back(peaks_container::value_type(mass, 1.0));
166  }
167 
170  nominal_mass_type nominalMass = 0) :
171  peaks_(peaks),
172  nominal_mass_(nominalMass)
173  {}
174 
177  peaks_(distribution.peaks_),
178  nominal_mass_(distribution.nominal_mass_)
179  {}
180 
183  {}
184 
191  size_type size() const { return std::min(peaks_.size(), SIZE); }
192 
199  IMSIsotopeDistribution & operator=(
200  const IMSIsotopeDistribution & distribution);
201 
209  bool operator==(const IMSIsotopeDistribution & distribution) const;
210 
218  bool operator!=(const IMSIsotopeDistribution & distribution) const;
219 
230  IMSIsotopeDistribution & operator*=(
231  const IMSIsotopeDistribution & distribution);
232 
243  IMSIsotopeDistribution & operator*=(unsigned int pow);
244 
252  {
253  return peaks_[i].mass + nominal_mass_ + i;
254  }
255 
263  {
264  return peaks_[i].abundance;
265  }
266 
272  mass_type getAverageMass() const;
273 
279  nominal_mass_type getNominalMass() const { return nominal_mass_; }
280 
287  {
288  this->nominal_mass_ = nominalMass;
289  }
290 
296  masses_container getMasses() const;
297 
303  abundances_container getAbundances() const;
304 
310  void normalize();
311 
317  bool empty() const { return peaks_.empty(); }
318 
319 private:
322 
325 
327  void setMinimumSize_();
328  };
329 
336  OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os,
337  const IMSIsotopeDistribution & distribution);
338 
339  } // namespace ims
340 } // namespace OpenMS
341 
342 #endif // OPENMS_CHEMISTRY_MASSDECOMPOSITION_IMS_ISOTOPE_DISTRIBUTION_H
Peak peak_type
Type of isotope peak.
Definition: IMSIsotopeDistribution.h:118
Structure that represents an isotope peak - pair of mass and abundance.
Definition: IMSIsotopeDistribution.h:102
IMSIsotopeDistribution(const IMSIsotopeDistribution &distribution)
Copy constructor.
Definition: IMSIsotopeDistribution.h:176
std::vector< abundance_type > abundances_container
Type of container with isotope abundances.
Definition: IMSIsotopeDistribution.h:142
IMSIsotopeDistribution(mass_type mass)
Constructor with single isotope.
Definition: IMSIsotopeDistribution.h:162
std::vector< mass_type > masses_container
Type of container with isotope masses.
Definition: IMSIsotopeDistribution.h:133
static size_type SIZE
Length of isotope distribution.
Definition: IMSIsotopeDistribution.h:154
nominal_mass_type nominal_mass_
Nominal mass of distribution.
Definition: IMSIsotopeDistribution.h:324
masses_container::const_iterator const_masses_iterator
Type of const iterator over container with isotope masses.
Definition: IMSIsotopeDistribution.h:139
double mass_type
Type of isotope mass.
Definition: IMSIsotopeDistribution.h:93
IMSIsotopeDistribution(nominal_mass_type nominalMass=0)
Constructor with nominal mass.
Definition: IMSIsotopeDistribution.h:157
mass_type mass
Definition: IMSIsotopeDistribution.h:113
Represents a distribution of isotopes restricted to the first K elements.
Definition: IMSIsotopeDistribution.h:88
OPENSWATHALGO_DLLAPI void normalize(const std::vector< double > &intensities, double normalization_factor, std::vector< double > &normalized_intensities)
Normalize intensities in vector by normalization_factor.
mass_type getMass(size_type i) const
Definition: IMSIsotopeDistribution.h:251
IMSIsotopeDistribution(const peaks_container &peaks, nominal_mass_type nominalMass=0)
Constructor with isotopes and nominal mass.
Definition: IMSIsotopeDistribution.h:169
void setNominalMass(nominal_mass_type nominalMass)
Definition: IMSIsotopeDistribution.h:286
peaks_container::const_iterator const_peaks_iterator
Type of const iterator over container with peaks.
Definition: IMSIsotopeDistribution.h:127
peaks_container::size_type size_type
Type of peaks container&#39;s size.
Definition: IMSIsotopeDistribution.h:130
double abundance_type
Type of isotope abundance.
Definition: IMSIsotopeDistribution.h:96
abundance_type abundance
Definition: IMSIsotopeDistribution.h:114
std::vector< peak_type > peaks_container
Type of container to store peaks.
Definition: IMSIsotopeDistribution.h:121
masses_container::iterator masses_iterator
Type of iterator over container with isotope masses.
Definition: IMSIsotopeDistribution.h:136
~IMSIsotopeDistribution()
Destructor.
Definition: IMSIsotopeDistribution.h:182
abundances_container::const_iterator const_abundances_iterator
Type of const iterator over container with isotope abundances.
Definition: IMSIsotopeDistribution.h:148
static abundance_type ABUNDANCES_SUM_ERROR
Error to be allowed for isotope distribution.
Definition: IMSIsotopeDistribution.h:151
unsigned int nominal_mass_type
Type of isotope nominal mass.
Definition: IMSIsotopeDistribution.h:99
abundance_type getAbundance(size_type i) const
Definition: IMSIsotopeDistribution.h:262
size_type size() const
Definition: IMSIsotopeDistribution.h:191
nominal_mass_type getNominalMass() const
Definition: IMSIsotopeDistribution.h:279
bool operator==(const Peak &peak) const
Definition: IMSIsotopeDistribution.h:108
bool empty() const
Definition: IMSIsotopeDistribution.h:317
peaks_container peaks_
Container for isotopes.
Definition: IMSIsotopeDistribution.h:321
peaks_container::iterator peaks_iterator
Type of iterator over container with peaks.
Definition: IMSIsotopeDistribution.h:124
abundances_container::iterator abundances_iterator
Type of iterator over container with isotope abundances.
Definition: IMSIsotopeDistribution.h:145
Peak(mass_type mass=0.0, abundance_type abundance=0.0)
Definition: IMSIsotopeDistribution.h:104
std::ostream & operator<<(std::ostream &os, const IMSAlphabet &alphabet)

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:15 using doxygen 1.8.5