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IonizationSimulation.h
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31 // $Maintainer: Chris Bielow$
32 // $Authors: Stephan Aiche, Chris Bielow$
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34 
35 #ifndef OPENMS_SIMULATION_IONIZATIONSIMULATION_H
36 #define OPENMS_SIMULATION_IONIZATIONSIMULATION_H
37 
43 
44 // STL includes
45 #include <set>
46 
47 namespace OpenMS
48 {
49 
64  class OPENMS_DLLAPI IonizationSimulation :
65  public DefaultParamHandler,
66  public ProgressLogger
67  {
68 
69 public:
71  typedef enum
72  {
74  ESI
75  } IonizationType;
76 
82 
85 
87  virtual ~IonizationSimulation();
89 
91  IonizationSimulation & operator=(const IonizationSimulation & source);
92 
103  void ionize(FeatureMapSim & features, ConsensusMap & charge_consensus, MSSimExperiment & experiment);
104 
105 private:
108 
109  class CompareCmpByEF_;
110 
112  void ionizeEsi_(FeatureMapSim &, ConsensusMap & charge_consensus);
113 
115  void ionizeMaldi_(FeatureMapSim &, ConsensusMap & charge_consensus);
116 
118  inline bool isFeatureValid_(const Feature & feature);
119 
121  void setFeatureProperties_(Feature & f,
122  const DoubleReal & adduct_mass,
123  const String & adduct_formula,
124  const SimChargeType charge,
125  const SimIntensityType new_intensity,
126  const Size parent_index);
127 
129  void setDefaultParams_();
130 
132  void updateMembers_();
133 
139  UInt countIonizedResidues_(const AASequence &) const;
140 
141 
142  // Members //
143 
146 
147  /*
148  @brief List of residues that are counted as basic during execution of countBasicResidues_
149 */
150  std::set<String> basic_residues_;
151 
156 
160  // important: leave that as vector<double> because gsl expects 'double' and not 'DoubleReal' (which might be something different)
161  std::vector<double> esi_impurity_probabilities_;
162 
163 
168 
173 
177  // important: leave that as vector<double> because gsl expects 'double' and not 'DoubleReal' (which might be something different)
178  std::vector<double> maldi_probabilities_;
179 
184 
185 protected:
188  };
189 
190 }
191 
192 #endif
Feature::ChargeType SimChargeType
Charge of a peptide.
Definition: SimTypes.h:65
A more convenient string class.
Definition: String.h:56
Simulates Protein ionization.
Definition: IonizationSimulation.h:64
A container for features.
Definition: FeatureMap.h:111
IonizationType
possible ionization methods
Definition: IonizationSimulation.h:71
A container for consensus elements.
Definition: ConsensusMap.h:60
Representation of a peptide/protein sequence.
Definition: AASequence.h:84
std::vector< Adduct > AdductsType
Definition: Adduct.h:50
Size max_adduct_charge_
Maximal charge that any impure adduct from parameter list has.
Definition: IonizationSimulation.h:172
std::vector< double > esi_impurity_probabilities_
Discrete distribution of impure charge adducts like Na+, K+, Ca++ etc besides the usual H+...
Definition: IonizationSimulation.h:161
std::set< String > basic_residues_
Definition: IonizationSimulation.h:150
SimCoordinateType minimal_mz_measurement_limit_
Minimum m/z detected by mass analyser.
Definition: IonizationSimulation.h:183
Adduct::AdductsType esi_adducts_
Corresponding table to esi_impurity_probabilities_ holding the actual element and its charge...
Definition: IonizationSimulation.h:167
std::vector< double > maldi_probabilities_
Preprocessed table of discrete distribution (MALDI charges)
Definition: IonizationSimulation.h:178
An LC-MS feature.
Definition: Feature.h:66
IonizationType ionization_type_
ESI or MALDI ionization.
Definition: IonizationSimulation.h:145
Wrapper class for random number generators used by the simulation classes.
Definition: SimTypes.h:99
Peak2D::IntensityType SimIntensityType
Abundance of proteins/peptides.
Definition: SimTypes.h:62
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
Base class for all classes that want to report their progess.
Definition: ProgressLogger.h:56
DoubleReal esi_probability_
Probability for the binomial distribution of ESI charge states.
Definition: IonizationSimulation.h:155
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:90
SimCoordinateType maximal_mz_measurement_limit_
Maximum m/z detected by mass analyser.
Definition: IonizationSimulation.h:181
SimRandomNumberGenerator const * rnd_gen_
Random number generator.
Definition: IonizationSimulation.h:187
Definition: IonizationSimulation.h:73

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