OpenMS
MetaboliteSpectralMatching Class Reference

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

Inheritance diagram for MetaboliteSpectralMatching:
[legend]
Collaboration diagram for MetaboliteSpectralMatching:
[legend]

Public Member Functions

 MetaboliteSpectralMatching ()
 Default constructor. More...
 
 ~MetaboliteSpectralMatching () override
 Default destructor. More...
 
void run (PeakMap &, PeakMap &, MzTab &, String &)
 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...
 
DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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...
 
virtual ~ProgressLogger ()
 Destructor. More...
 
 ProgressLogger (const ProgressLogger &other)
 Copy constructor. More...
 
ProgressLoggeroperator= (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 setLogger (ProgressLoggerImpl *logger)
 Sets the logger to be used for progress logging. 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 (UInt64 bytes_processed=0) const
 
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...
 
- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. 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)
 

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_
 
bool merge_spectra_
 

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< Stringsubsections_
 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_
 
ProgressLoggerImplcurrent_logger_
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Constructor & Destructor Documentation

◆ MetaboliteSpectralMatching()

Default constructor.

◆ ~MetaboliteSpectralMatching()

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 
)
staticprotected

◆ exportMzTab_()

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

private member functions

◆ run()

void run ( PeakMap ,
PeakMap ,
MzTab ,
String  
)

◆ updateMembers_()

void updateMembers_ ( )
overrideprotectedvirtual

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

◆ merge_spectra_

bool merge_spectra_
private

◆ mz_error_unit_

String mz_error_unit_
private

◆ precursor_mz_error_

double precursor_mz_error_
private

◆ report_mode_

String report_mode_
private