OpenMS  2.4.0
TheoreticalSpectrumGeneratorXLMS.h
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31 // $Maintainer: Eugen Netz $
32 // $Authors: Eugen Netz $
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34 
35 
36 #pragma once
37 
43 
44 
45 namespace OpenMS
46 {
47  class AASequence;
48 
56  class OPENMS_DLLAPI TheoreticalSpectrumGeneratorXLMS :
57  public DefaultParamHandler
58  {
59  public:
60 
61  struct LossMass
62  {
64  double mass;
65 
66  bool operator==(const LossMass & other) const
67  {
68  return name == other.name && mass == other.mass;
69  }
70  };
71 
76  {
77  bool operator() (const LossMass& a, const LossMass& b)
78  {
79  return a.mass < b.mass;
80  }
81  };
82 
83 
89 
92 
96 
99 
116  virtual void getLinearIonSpectrum(PeakSpectrum & spectrum, AASequence & peptide, Size link_pos, bool frag_alpha, int charge = 1, Size link_pos_2 = 0) const;
117 
141  virtual void getXLinkIonSpectrum(PeakSpectrum & spectrum, AASequence & peptide, Size link_pos, double precursor_mass, bool frag_alpha, int mincharge, int maxcharge, Size link_pos_2 = 0) const;
142 
162  virtual void getXLinkIonSpectrum(PeakSpectrum & spectrum, OPXLDataStructs::ProteinProteinCrossLink & crosslink, bool frag_alpha, int mincharge, int maxcharge) const;
163 
165  void updateMembers_() override;
166 
167  protected:
168 
183  virtual void addLinearPeaks_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, AASequence & peptide, Size link_pos, bool frag_alpha, Residue::ResidueType res_type, std::vector< std::set< LossMass, LossMassComparator > > & forward_losses, std::vector< std::set< LossMass, LossMassComparator > > & backward_losses, int charge = 1, Size link_pos_2 = 0) const;
184 
202  virtual void addPeak_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, double pos, double intensity, Residue::ResidueType res_type, Size ion_index, int charge, String ion_type) const;
203 
213  virtual void addPrecursorPeaks_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, double precursor_mass, int charge) const;
214 
229  virtual void addLinearIonLosses_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray& charges, DataArrays::StringDataArray& ion_names, double mono_weight, Residue::ResidueType res_type, Size frag_index, double intensity, int charge, String ion_type, std::set< LossMass, LossMassComparator > & losses) const;
230 
245  virtual void addXLinkIonLosses_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray& charges, DataArrays::StringDataArray& ion_names, double mono_weight, double intensity, int charge, String ion_name, std::set< LossMass, LossMassComparator > & losses) const;
246 
263  virtual void addKLinkedIonPeaks_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, AASequence & peptide, Size link_pos, double precursor_mass, bool frag_alpha, int charge) const;
264 
283  virtual void addXLinkIonPeaks_(PeakSpectrum& spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, AASequence & peptide, Size link_pos, double precursor_mass, bool frag_alpha, Residue::ResidueType res_type, std::vector< std::set< LossMass, LossMassComparator > > & forward_losses, std::vector< std::set< LossMass, LossMassComparator > > & backward_losses, int charge, Size link_pos_2 = 0) const;
284 
303  virtual void addXLinkIonPeaks_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, OPXLDataStructs::ProteinProteinCrossLink & crosslink, bool frag_alpha, Residue::ResidueType res_type, std::vector< std::set< LossMass, LossMassComparator > > & forward_losses, std::vector< std::set< LossMass, LossMassComparator > > & backward_losses, std::set< LossMass, LossMassComparator > & losses_peptide2, int charge) const;
304 
312  std::vector< std::set< LossMass, LossMassComparator > > getForwardLosses_(AASequence & peptide) const;
313 
321  std::vector< std::set< LossMass, LossMassComparator > > getBackwardLosses_(AASequence & peptide) const;
322 
323  // TODO copied from normal TSG, but it is protected over there. Move it to Residue class maybe?
325  char residueTypeToIonLetter_(Residue::ResidueType res_type) const;
326 
339  double a_intensity_;
340  double b_intensity_;
341  double c_intensity_;
342  double x_intensity_;
343  double y_intensity_;
344  double z_intensity_;
347  double pre_int_;
348  double pre_int_H2O_;
349  double pre_int_NH3_;
351  };
352 }
A more convenient string class.
Definition: String.h:57
bool operator==(const LossMass &other) const
Definition: TheoreticalSpectrumGeneratorXLMS.h:66
bool add_y_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:328
double c_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:341
bool add_b_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:327
Representation of a peptide/protein sequence.
Definition: AASequence.h:107
double pre_int_H2O_
Definition: TheoreticalSpectrumGeneratorXLMS.h:348
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
double pre_int_NH3_
Definition: TheoreticalSpectrumGeneratorXLMS.h:349
bool add_abundant_immonium_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:338
Integer data array class.
Definition: DataArrays.h:51
String name
Definition: TheoreticalSpectrumGeneratorXLMS.h:63
double a_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:339
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
Generates theoretical spectra for cross-linked peptides.
Definition: TheoreticalSpectrumGeneratorXLMS.h:56
bool add_first_prefix_ion_
Definition: TheoreticalSpectrumGeneratorXLMS.h:333
bool add_a_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:329
bool add_losses_
Definition: TheoreticalSpectrumGeneratorXLMS.h:334
double x_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:342
double y_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:343
bool add_x_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:331
Comparator to sort and filter LossMasses by mass.
Definition: TheoreticalSpectrumGeneratorXLMS.h:75
Definition: TheoreticalSpectrumGeneratorXLMS.h:61
Int max_isotope_
Definition: TheoreticalSpectrumGeneratorXLMS.h:345
double pre_int_
Definition: TheoreticalSpectrumGeneratorXLMS.h:347
ResidueType
Definition: Residue.h:150
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
double mass
Definition: TheoreticalSpectrumGeneratorXLMS.h:64
double z_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:344
bool add_c_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:330
double rel_loss_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:346
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
String data array class.
Definition: DataArrays.h:57
bool add_precursor_peaks_
Definition: TheoreticalSpectrumGeneratorXLMS.h:337
bool add_isotopes_
Definition: TheoreticalSpectrumGeneratorXLMS.h:336
int Int
Signed integer type.
Definition: Types.h:102
bool add_z_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:332
bool add_metainfo_
Definition: TheoreticalSpectrumGeneratorXLMS.h:335
double b_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:340
bool add_k_linked_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:350