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OpenMS
2.4.0
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68 return name == other.
name && mass == other.
mass;
116 virtual void getLinearIonSpectrum(
PeakSpectrum & spectrum,
AASequence & peptide,
Size link_pos,
bool frag_alpha,
int charge = 1,
Size link_pos_2 = 0)
const;
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;
165 void updateMembers_()
override;
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;
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;
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;
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;
312 std::vector< std::set< LossMass, LossMassComparator > > getForwardLosses_(
AASequence & peptide)
const;
321 std::vector< std::set< LossMass, LossMassComparator > > getBackwardLosses_(
AASequence & peptide)
const;
Integer data array class.
Definition: DataArrays.h:51
bool add_x_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:331
bool add_precursor_peaks_
Definition: TheoreticalSpectrumGeneratorXLMS.h:337
A more convenient string class.
Definition: String.h:57
Int max_isotope_
Definition: TheoreticalSpectrumGeneratorXLMS.h:345
String name
Definition: TheoreticalSpectrumGeneratorXLMS.h:63
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
double rel_loss_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:346
double x_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:342
bool add_y_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:328
bool operator==(const LossMass &other) const
Definition: TheoreticalSpectrumGeneratorXLMS.h:66
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
double mass
Definition: TheoreticalSpectrumGeneratorXLMS.h:64
int Int
Signed integer type.
Definition: Types.h:102
bool add_b_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:327
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool add_first_prefix_ion_
Definition: TheoreticalSpectrumGeneratorXLMS.h:333
bool add_isotopes_
Definition: TheoreticalSpectrumGeneratorXLMS.h:336
double z_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:344
The ProteinProteinCrossLink struct represents a cross-link between two peptides in OpenPepXL.
Definition: OPXLDataStructs.h:72
bool add_abundant_immonium_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:338
bool add_z_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:332
ResidueType
Definition: Residue.h:150
String data array class.
Definition: DataArrays.h:57
double a_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:339
bool add_a_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:329
Definition: TheoreticalSpectrumGeneratorXLMS.h:61
bool add_c_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:330
double y_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:343
bool add_losses_
Definition: TheoreticalSpectrumGeneratorXLMS.h:334
double pre_int_NH3_
Definition: TheoreticalSpectrumGeneratorXLMS.h:349
double c_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:341
double b_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:340
Representation of a peptide/protein sequence.
Definition: AASequence.h:107
Generates theoretical spectra for cross-linked peptides.
Definition: TheoreticalSpectrumGeneratorXLMS.h:56
double pre_int_H2O_
Definition: TheoreticalSpectrumGeneratorXLMS.h:348
bool add_metainfo_
Definition: TheoreticalSpectrumGeneratorXLMS.h:335
double pre_int_
Definition: TheoreticalSpectrumGeneratorXLMS.h:347
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
Comparator to sort and filter LossMasses by mass.
Definition: TheoreticalSpectrumGeneratorXLMS.h:75
bool add_k_linked_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:350