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CoarseIsotopePatternGenerator.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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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/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopePatternGenerator.h>
38 #include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
39
40 #include <set>
41
42 namespace OpenMS
43 {
96 class OPENMS_DLLAPI CoarseIsotopePatternGenerator
97 : public IsotopePatternGenerator
98 {
99
100 public:
101 CoarseIsotopePatternGenerator();
102
103 CoarseIsotopePatternGenerator(const Size& max_isotope);
104
105 CoarseIsotopePatternGenerator(const Size& max_isotope, const bool round_masses);
106
107 virtual ~CoarseIsotopePatternGenerator();
108
110
111
117 void setMaxIsotope(const Size& max_isotope);
118
120 void setRoundMasses(const bool round_masses);
121
123 Size getMaxIsotope() const;
124
126 bool getRoundMasses() const;
128
136 IsotopeDistribution run(const EmpiricalFormula&) const override;
137
144 IsotopeDistribution estimateFromPeptideWeight(double average_weight);
145
155 IsotopeDistribution estimateFromPeptideWeightAndS(double average_weight, UInt S);
156
163 IsotopeDistribution estimateFromRNAWeight(double average_weight);
164
170 IsotopeDistribution estimateFromDNAWeight(double average_weight);
171
177 IsotopeDistribution estimateFromWeightAndComp(double average_weight, double C, double H, double N, double O, double S, double P);
178
193 IsotopeDistribution estimateFromWeightAndCompAndS(double average_weight, UInt S, double C, double H, double N, double O, double P);
194
209 IsotopeDistribution estimateForFragmentFromPeptideWeight(double average_weight_precursor, double average_weight_fragment, const std::set<UInt>& precursor_isotopes);
210
230 IsotopeDistribution estimateForFragmentFromPeptideWeightAndS(double average_weight_precursor, UInt S_precursor, double average_weight_fragment, UInt S_fragment, const std::set<UInt>& precursor_isotopes);
231
246 IsotopeDistribution estimateForFragmentFromRNAWeight(double average_weight_precursor, double average_weight_fragment, const std::set<UInt>& precursor_isotopes);
247
262 IsotopeDistribution estimateForFragmentFromDNAWeight(double average_weight_precursor, double average_weight_fragment, const std::set<UInt>& precursor_isotopes);
263
285 IsotopeDistribution estimateForFragmentFromWeightAndComp(double average_weight_precursor, double average_weight_fragment, const std::set<UInt>& precursor_isotopes, double C, double H, double N, double O, double S, double P);
286
305 IsotopeDistribution calcFragmentIsotopeDist(const IsotopeDistribution& fragment_isotope_dist, const IsotopeDistribution& comp_fragment_isotope_dist, const std::set<UInt>& precursor_isotopes, const double fragment_mono_mass) const;
306
307 CoarseIsotopePatternGenerator& operator=(const CoarseIsotopePatternGenerator& iso);
308
310 IsotopeDistribution::ContainerType convolve_(const IsotopeDistribution::ContainerType & left, const IsotopeDistribution::ContainerType & right) const;
311
313 IsotopeDistribution::ContainerType convolvePow_(const IsotopeDistribution::ContainerType & input, Size factor) const;
314
316 IsotopeDistribution::ContainerType convolveSquare_(const IsotopeDistribution::ContainerType & input) const;
317
319 IsotopeDistribution::ContainerType correctMass_(const IsotopeDistribution::ContainerType & input, const double mono_weight) const;
320
321 protected:
322
329 IsotopeDistribution calcFragmentIsotopeDist_(const IsotopeDistribution::ContainerType& fragment_isotope_dist, const IsotopeDistribution::ContainerType& comp_fragment_isotope_dist, const std::set<UInt>& precursor_isotopes) const;
330
332 IsotopeDistribution::ContainerType fillGaps_(const IsotopeDistribution::ContainerType& id) const;
333
334 protected:
336 Size max_isotope_;
338 bool round_masses_;
339
340 };
341
342 } // namespace OpenMS
343
OpenMS::CoarseIsotopePatternGenerator::max_isotope_
Size max_isotope_
maximal isotopes which is used to calculate the distribution
Definition: CoarseIsotopePatternGenerator.h:336
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:64
IsotopeDistribution.h
OpenMS::CoarseIsotopePatternGenerator::round_masses_
bool round_masses_
flag to determine whether masses should be rounded or not
Definition: CoarseIsotopePatternGenerator.h:338
IsotopePatternGenerator.h
OpenMS::IsotopePatternGenerator
Provides an interface for different isotope pattern generator methods.
Definition: IsotopePatternGenerator.h:53
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:82
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::CoarseIsotopePatternGenerator
Isotope pattern generator for coarse isotope distributions.
Definition: CoarseIsotopePatternGenerator.h:96
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::IsotopeDistribution::ContainerType
std::vector< MassAbundance > ContainerType
Definition: IsotopeDistribution.h:72