OpenMS
Static Public Member Functions | Static Public Attributes | List of all members
NuXLFragmentIonGenerator Class Reference

#include <OpenMS/ANALYSIS/NUXL/NuXLFragmentIonGenerator.h>

Collaboration diagram for NuXLFragmentIonGenerator:
[legend]

Static Public Member Functions

static void addMS2MarkerIons (const std::vector< NuXLFragmentAdductDefinition > &marker_ions, PeakSpectrum &spectrum, PeakSpectrum::IntegerDataArray &spectrum_charge, PeakSpectrum::StringDataArray &spectrum_annotation)
 
static void addShiftedImmoniumIons (const String &unmodified_sequence, const String &fragment_shift_name, const double fragment_shift_mass, PeakSpectrum &partial_loss_spectrum, PeakSpectrum::IntegerDataArray &partial_loss_spectrum_charge, PeakSpectrum::StringDataArray &partial_loss_spectrum_annotation)
 
static void generatePartialLossSpectrum (const String &unmodified_sequence, const double &fixed_and_variable_modified_peptide_weight, const String &precursor_rna_adduct, const double &precursor_rna_mass, const int &precursor_charge, const std::vector< NuXLFragmentAdductDefinition > &partial_loss_modification, const PeakSpectrum &patial_loss_template_z1, const PeakSpectrum &patial_loss_template_z2, const PeakSpectrum &patial_loss_template_z3, PeakSpectrum &partial_loss_spectrum)
 
static void addPrecursorWithCompleteRNA_ (const double fixed_and_variable_modified_peptide_weight, const String &precursor_rna_adduct, const double precursor_rna_mass, const int charge, PeakSpectrum &partial_loss_spectrum, MSSpectrum::IntegerDataArray &partial_loss_spectrum_charge, MSSpectrum::StringDataArray &partial_loss_spectrum_annotation)
 
static void addSpecialLysImmonumIons (const String &unmodified_sequence, PeakSpectrum &spectrum, PeakSpectrum::IntegerDataArray &spectrum_charge, PeakSpectrum::StringDataArray &spectrum_annotation)
 

Static Public Attributes

static constexpr const char * ANNOTATIONS_MARKER_ION_PREFIX = "MI:"
 

Member Function Documentation

◆ addMS2MarkerIons()

static void addMS2MarkerIons ( const std::vector< NuXLFragmentAdductDefinition > &  marker_ions,
PeakSpectrum &  spectrum,
PeakSpectrum::IntegerDataArray &  spectrum_charge,
PeakSpectrum::StringDataArray &  spectrum_annotation 
)
static

◆ addPrecursorWithCompleteRNA_()

static void addPrecursorWithCompleteRNA_ ( const double  fixed_and_variable_modified_peptide_weight,
const String &  precursor_rna_adduct,
const double  precursor_rna_mass,
const int  charge,
PeakSpectrum &  partial_loss_spectrum,
MSSpectrum::IntegerDataArray &  partial_loss_spectrum_charge,
MSSpectrum::StringDataArray &  partial_loss_spectrum_annotation 
)
static

◆ addShiftedImmoniumIons()

static void addShiftedImmoniumIons ( const String &  unmodified_sequence,
const String &  fragment_shift_name,
const double  fragment_shift_mass,
PeakSpectrum &  partial_loss_spectrum,
PeakSpectrum::IntegerDataArray &  partial_loss_spectrum_charge,
PeakSpectrum::StringDataArray &  partial_loss_spectrum_annotation 
)
static

◆ addSpecialLysImmonumIons()

static void addSpecialLysImmonumIons ( const String &  unmodified_sequence,
PeakSpectrum &  spectrum,
PeakSpectrum::IntegerDataArray &  spectrum_charge,
PeakSpectrum::StringDataArray &  spectrum_annotation 
)
static

◆ generatePartialLossSpectrum()

static void generatePartialLossSpectrum ( const String &  unmodified_sequence,
const double &  fixed_and_variable_modified_peptide_weight,
const String &  precursor_rna_adduct,
const double &  precursor_rna_mass,
const int &  precursor_charge,
const std::vector< NuXLFragmentAdductDefinition > &  partial_loss_modification,
const PeakSpectrum &  patial_loss_template_z1,
const PeakSpectrum &  patial_loss_template_z2,
const PeakSpectrum &  patial_loss_template_z3,
PeakSpectrum &  partial_loss_spectrum 
)
static

Member Data Documentation

◆ ANNOTATIONS_MARKER_ION_PREFIX

constexpr const char* ANNOTATIONS_MARKER_ION_PREFIX = "MI:"
staticconstexpr