RNPxlSearch::RNPxlFragmentIonGenerator Class Reference

Static Public Member Functions
static void	addMS2MarkerIons (const vector< FragmentAdductDefinition_ > &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 AASequence &fixed_and_variable_modified_peptide, const double &fixed_and_variable_modified_peptide_weight, const String &precursor_rna_adduct, const double &precursor_rna_weight, const int &precursor_charge, const vector< FragmentAdductDefinition_ > &partial_loss_modification, const TheoreticalSpectrumGenerator &partial_loss_spectrum_generator, PeakSpectrum &partial_loss_spectrum)
static void	addPrecursorWithCompleteRNA_ (const double fixed_and_variable_modified_peptide_weight, const String &precursor_rna_adduct, const double precursor_rna_weight, 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)

Member Function Documentation

addMS2MarkerIons()

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

static

References OpenMS::Constants::PROTON_MASS_U.

addPrecursorWithCompleteRNA_()

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

static

References OpenMS::Constants::PROTON_MASS_U.

addShiftedImmoniumIons()

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

References RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon(), EmpiricalFormula::getMonoWeight(), and String::hasSubstring().

addSpecialLysImmonumIons()

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

static

References EmpiricalFormula::getMonoWeight(), and String::has().

generatePartialLossSpectrum()

void generatePartialLossSpectrum ( const String &  unmodified_sequence, const AASequence &  fixed_and_variable_modified_peptide, const double &  fixed_and_variable_modified_peptide_weight, const String &  precursor_rna_adduct, const double &  precursor_rna_weight, const int &  precursor_charge, const vector< FragmentAdductDefinition_ > &  partial_loss_modification, const TheoreticalSpectrumGenerator &  partial_loss_spectrum_generator, PeakSpectrum &  partial_loss_spectrum  )

static

References MSSpectrum::getIntegerDataArrays(), Peak1D::getMZ(), TheoreticalSpectrumGenerator::getSpectrum(), MSSpectrum::getStringDataArrays(), Peak1D::setMZ(), and MSSpectrum::sortByPosition().