| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | Protected Member Functions | Static Protected Member Functions | Private Member Functions | Private Attributes | List of all members
MetaboliteSpectralMatching Class Reference

`#include <OpenMS/ANALYSIS/ID/MetaboliteSpectralMatching.h>`

Inheritance diagram for MetaboliteSpectralMatching:

## Public Member Functions

| MetaboliteSpectralMatching ()
| Default constructor. More...
| ~MetaboliteSpectralMatching () override
| Default destructor. More...
void | run (PeakMap &, PeakMap &, MzTab &)
| main method of MetaboliteSpectralMatching 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...
Public Member Functions inherited from ProgressLogger
| ProgressLogger ()
| Constructor. More...
| ~ProgressLogger ()
| Destructor. More...
| ProgressLogger (const ProgressLogger &other)
| Copy constructor. More...
ProgressLogger & | operator= (const ProgressLogger &other)
| Assignment Operator. More...
void | setLogType (LogType type) const
| Sets the progress log that should be used. The default type is NONE! More...
LogType | getLogType () const
| Returns the type of progress log being used. More...
void | startProgress (SignedSize begin, SignedSize end, const String &label) const
| Initializes the progress display. More...
void | setProgress (SignedSize value) const
| Sets the current progress. More...
void | endProgress () const
| Ends the progress display. More...
void | nextProgress () const
| increment progress by 1 (according to range begin-end) More...

## Static Public Member Functions

static double | computeHyperScore (double fragment_mass_error, bool fragment_mass_tolerance_unit_ppm, const MSSpectrum &exp_spectrum, const MSSpectrum &db_spectrum, double mz_lower_bound=0.0)
| hyperscore computation More...
static double | computeHyperScore (double fragment_mass_error, bool fragment_mass_tolerance_unit_ppm, const MSSpectrum &exp_spectrum, const MSSpectrum &db_spectrum, std::vector< PeptideHit::PeakAnnotation > &annotations, double mz_lower_bound=0.0)
| hyperscore computation (with output of peak annotations) More...

## Protected Member Functions

void | updateMembers_ () override
| This method is used to update extra member variables at the end of the setParameters() method. More...
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Static Protected Member Functions

static double | computeHyperScore_ (double fragment_mass_error, bool fragment_mass_tolerance_unit_ppm, const MSSpectrum &exp_spectrum, const MSSpectrum &db_spectrum, std::vector< PeptideHit::PeakAnnotation > *annotations=0, double mz_lower_bound=0.0)
Static Protected Member Functions inherited from ProgressLogger
static String | logTypeToFactoryName_ (LogType type)
| Return the name of the factory product used for this log type. More...

## Private Member Functions

void | exportMzTab_ (const std::vector< SpectralMatch > &, MzTab &)
| private member functions More...

## Private Attributes

double | precursor_mz_error_
double | fragment_mz_error_
String | mz_error_unit_
String | ion_mode_
String | report_mode_

## Additional Inherited Members

Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. More...
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...
Protected Attributes inherited from ProgressLogger
LogType | type_
time_t | last_invoke_
ProgressLoggerImpl * | current_logger_
Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_

## Constructor & Destructor Documentation

## ◆ MetaboliteSpectralMatching()

MetaboliteSpectralMatching | ( |  | ) |

Default constructor.

## ◆ ~MetaboliteSpectralMatching()

~MetaboliteSpectralMatching | ( |  | ) |

override

Default destructor.

## Member Function Documentation

## ◆ computeHyperScore() [1/2]

static double computeHyperScore | ( | double | fragment_mass_error,
|  | bool | fragment_mass_tolerance_unit_ppm,
|  | const MSSpectrum & | exp_spectrum,
|  | const MSSpectrum & | db_spectrum,
|  | double | mz_lower_bound = `0.0`
| ) |  |

static

hyperscore computation

Referenced by NucleicAcidSearchEngine::main_().

## ◆ computeHyperScore() [2/2]

static double computeHyperScore | ( | double | fragment_mass_error,
|  | bool | fragment_mass_tolerance_unit_ppm,
|  | const MSSpectrum & | exp_spectrum,
|  | const MSSpectrum & | db_spectrum,
|  | std::vector< PeptideHit::PeakAnnotation > & | annotations,
|  | double | mz_lower_bound = `0.0`
| ) |  |

static

hyperscore computation (with output of peak annotations)

## ◆ computeHyperScore_()

static double computeHyperScore_ | ( | double | fragment_mass_error,
|  | bool | fragment_mass_tolerance_unit_ppm,
|  | const MSSpectrum & | exp_spectrum,
|  | const MSSpectrum & | db_spectrum,
|  | std::vector< PeptideHit::PeakAnnotation > * | annotations = `0`,
|  | double | mz_lower_bound = `0.0`
| ) |  |

static protected

## ◆ exportMzTab_()

void exportMzTab_ | ( | const std::vector< SpectralMatch > & | ,
|  | MzTab & |
| ) |  |

private

private member functions

## ◆ run()

void run | ( | PeakMap & | ,
|  | PeakMap & | ,
|  | MzTab & |
| ) |  |

main method of MetaboliteSpectralMatching

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ fragment_mz_error_

double fragment_mz_error_

private

## ◆ ion_mode_

String ion_mode_

private

## ◆ mz_error_unit_

String mz_error_unit_

private

## ◆ precursor_mz_error_

double precursor_mz_error_

private

## ◆ report_mode_

String report_mode_

private