| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
NucleicAcidSpectrumGenerator Class Reference
Chemistry

Generates theoretical spectra for nucleic acid sequences. More...

`#include <OpenMS/CHEMISTRY/NucleicAcidSpectrumGenerator.h>`

Inheritance diagram for NucleicAcidSpectrumGenerator:

## Public Member Functions

NucleicAcidSpectrumGenerator & | operator= (const NucleicAcidSpectrumGenerator &source)
| assignment operator More...
Constructors and Destructors
| NucleicAcidSpectrumGenerator ()
| default constructor More...
| NucleicAcidSpectrumGenerator (const NucleicAcidSpectrumGenerator &source)
| copy constructor More...
| ~NucleicAcidSpectrumGenerator () override
| destructor More...
Acessors
void | getSpectrum (MSSpectrum &spectrum, const NASequence &oligo, Int min_charge, Int max_charge) const
| Generates a spectrum for an oligonucleotide sequence, with the ion types that are set in the tool parameters. More...
void | getMultipleSpectra (std::map< Int, MSSpectrum > &spectra, const NASequence &oligo, const std::set< Int > &charges, Int base_charge=1) const
| Generates spectra in multiple charge states for an oligonucleotide sequence. More...
void | updateMembers_ () override
| overwrite More...
Public Member Functions inherited from DefaultParamHandler
| DefaultParamHandler (const String &name)
| Constructor with name that is displayed in error messages. More...
| DefaultParamHandler (const DefaultParamHandler &rhs)
| Copy constructor. More...
virtual | ~DefaultParamHandler ()
| Destructor. More...
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs)
| Assignment operator. More...
virtual bool | operator== (const DefaultParamHandler &rhs) const
| Equality operator. More...
void | setParameters (const Param &param)
| Sets the parameters. More...
const Param & | getParameters () const
| Non-mutable access to the parameters. More...
const Param & | getDefaults () const
| Non-mutable access to the default parameters. More...
const String & | getName () const
| Non-mutable access to the name. More...
void | setName (const String &name)
| Mutable access to the name. More...
const std::vector< String > & | getSubsections () const
| Non-mutable access to the registered subsections. More...

## Protected Member Functions

void | addFragmentPeaks_ (MSSpectrum &spectrum, const std::vector< double > &fragment_masses, const String &ion_type, double offset, double intensity, Size start=0) const
| Helper function to add (uncharged) fragment peaks to a spectrum. More...
void | addAMinusBPeaks_ (MSSpectrum &spectrum, const std::vector< double > &fragment_masses, const NASequence &oligo, Size start=0) const
| Special version of addFragmentPeaks_() for a-B ions. More...
MSSpectrum | getUnchargedSpectrum_ (const NASequence &oligo) const
| Generates a spectrum containing peaks for uncharged fragment masses. More...
void | addChargedSpectrum_ (MSSpectrum &spectrum, const MSSpectrum &uncharged_spectrum, Int charge, bool add_precursor) const
| Adds a charged version of an uncharged spectrum to another spectrum. More...
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Protected Attributes

bool | add_a_ions_
bool | add_b_ions_
bool | add_c_ions_
bool | add_d_ions_
bool | add_w_ions_
bool | add_x_ions_
bool | add_y_ions_
bool | add_z_ions_
bool | add_aB_ions_
bool | add_first_prefix_ion_
bool | add_metainfo_
bool | add_precursor_peaks_
bool | add_all_precursor_charges_
double | a_intensity_
double | b_intensity_
double | c_intensity_
double | d_intensity_
double | w_intensity_
double | x_intensity_
double | y_intensity_
double | z_intensity_
double | aB_intensity_
double | precursor_intensity_
Protected Attributes inherited from DefaultParamHandler
Param | param_
| Container for current parameters. More...
Param | defaults_
| Container for default parameters. This member should be filled in the constructor of derived classes! More...
std::vector< String > | subsections_
| Container for registered subsections. This member should be filled in the constructor of derived classes! More...
String | error_name_
| Name that is displayed in error messages during the parameter checking. More...
bool | check_defaults_
| If this member is set to false no checking if parameters in done;. More...
bool | warn_empty_defaults_
| If this member is set to false no warning is emitted when defaults are empty;. More...

## Detailed Description

Generates theoretical spectra for nucleic acid sequences.

## Constructor & Destructor Documentation

## ◆ NucleicAcidSpectrumGenerator() [1/2]

NucleicAcidSpectrumGenerator | ( |  | ) |

default constructor

## ◆ NucleicAcidSpectrumGenerator() [2/2]

NucleicAcidSpectrumGenerator | ( | const NucleicAcidSpectrumGenerator & | source | ) |

copy constructor

## ◆ ~NucleicAcidSpectrumGenerator()

~NucleicAcidSpectrumGenerator | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ addAMinusBPeaks_()

void addAMinusBPeaks_ | ( | MSSpectrum & | spectrum,
|  | const std::vector< double > & | fragment_masses,
|  | const NASequence & | oligo,
|  | Size | start = `0`
| ) |  | const

protected

Special version of addFragmentPeaks_() for a-B ions.

## ◆ addChargedSpectrum_()

void addChargedSpectrum_ | ( | MSSpectrum & | spectrum,
|  | const MSSpectrum & | uncharged_spectrum,
|  | Int | charge,
|  | bool | add_precursor
| ) |  | const

protected

Adds a charged version of an uncharged spectrum to another spectrum.

## ◆ addFragmentPeaks_()

void addFragmentPeaks_ | ( | MSSpectrum & | spectrum,
|  | const std::vector< double > & | fragment_masses,
|  | const String & | ion_type,
|  | double | offset,
|  | double | intensity,
|  | Size | start = `0`
| ) |  | const

protected

Helper function to add (uncharged) fragment peaks to a spectrum.

## ◆ getMultipleSpectra()

void getMultipleSpectra | ( | std::map< Int, MSSpectrum > & | spectra,
|  | const NASequence & | oligo,
|  | const std::set< Int > & | charges,
|  | Int | base_charge = `1`
| ) |  | const

Generates spectra in multiple charge states for an oligonucleotide sequence.

Parameters

  spectra | Output spectra
  oligo | Target oligonucleotide sequence
  charges | Set of charge states to generate
  base_charge | Minimum charge for peaks in each spectrum

One spectrum per element in `charges` is generated in `spectra`.

All values in `charges` must be either positive or negative.

This function is more efficient than calling getSpectrum() multiple times, because spectra of lower charge states are reused.

Referenced by NucleicAcidSearchEngine::main_().

## ◆ getSpectrum()

void getSpectrum | ( | MSSpectrum & | spectrum,
|  | const NASequence & | oligo,
|  | Int | min_charge,
|  | Int | max_charge
| ) |  | const

Generates a spectrum for an oligonucleotide sequence, with the ion types that are set in the tool parameters.

## ◆ getUnchargedSpectrum_()

MSSpectrum getUnchargedSpectrum_ | ( | const NASequence & | oligo | ) | const

protected

Generates a spectrum containing peaks for uncharged fragment masses.

## ◆ operator=()

NucleicAcidSpectrumGenerator& operator= | ( | const NucleicAcidSpectrumGenerator & | source | ) |

assignment operator

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override virtual

overwrite

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ a_intensity_

double a_intensity_

protected

## ◆ aB_intensity_

double aB_intensity_

protected

## ◆ add_a_ions_

bool add_a_ions_

protected

## ◆ add_aB_ions_

bool add_aB_ions_

protected

## ◆ add_all_precursor_charges_

bool add_all_precursor_charges_

protected

## ◆ add_b_ions_

bool add_b_ions_

protected

## ◆ add_c_ions_

bool add_c_ions_

protected

## ◆ add_d_ions_

bool add_d_ions_

protected

## ◆ add_first_prefix_ion_

bool add_first_prefix_ion_

protected

## ◆ add_metainfo_

bool add_metainfo_

protected

## ◆ add_precursor_peaks_

bool add_precursor_peaks_

protected

## ◆ add_w_ions_

bool add_w_ions_

protected

## ◆ add_x_ions_

bool add_x_ions_

protected

## ◆ add_y_ions_

bool add_y_ions_

protected

## ◆ add_z_ions_

bool add_z_ions_

protected

## ◆ b_intensity_

double b_intensity_

protected

## ◆ c_intensity_

double c_intensity_

protected

## ◆ d_intensity_

double d_intensity_

protected

## ◆ precursor_intensity_

double precursor_intensity_

protected

## ◆ w_intensity_

double w_intensity_

protected

## ◆ x_intensity_

double x_intensity_

protected

## ◆ y_intensity_

double y_intensity_

protected

## ◆ z_intensity_

double z_intensity_

protected