#include <OpenMS/ANALYSIS/TOPDOWN/FLASHTnTAlgorithm.h>

Inheritance diagram for FLASHTnTAlgorithm:

Collaboration diagram for FLASHTnTAlgorithm:

Public Member Functions
	FLASHTnTAlgorithm ()
	constructor More...

	~FLASHTnTAlgorithm () override=default
	destructor More...

	FLASHTnTAlgorithm (const FLASHTnTAlgorithm &)
	copy constructor More...

	FLASHTnTAlgorithm (FLASHTnTAlgorithm &&other)=default
	move constructor More...

FLASHTnTAlgorithm &	operator= (const FLASHTnTAlgorithm &other)
	assignment operator More...

void	run (const MSExperiment &map, const std::vector< FASTAFile::FASTAEntry > &fasta_entry)
	Find sequence tags from `mzs` and `intensities` then store them in `tags`. More...

void	getProteoformHitsMatchedBy (const FLASHHelperClasses::Tag &tag, std::vector< ProteinHit > &hits) const

void	getTags (std::vector< FLASHHelperClasses::Tag > &tags) const

void	getProteoforms (std::vector< ProteinHit > &hits) const

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...

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...

virtual	~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	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...

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	setDefaultParams_ ()
	implemented for DefaultParamHandler More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Private Member Functions
bool	areConsistent_ (const ProteinHit &a, const ProteinHit &b, double tol) const

void	markRepresentativeProteoformHits_ (double tol)

Private Attributes
Param	tagger_param_

Param	extender_param_

double	decoy_factor_ = 0

double	prsm_fdr_ = 1

double	pro_fdr_ = 1

bool	keep_decoy_ = false

bool	keep_underdetermined_ = true

bool	multiple_hits_per_spec_ = false

std::vector< ProteinHit >	proteoform_hits_

std::vector< FLASHHelperClasses::Tag >	tags_

std::map< int, std::vector< int > >	matching_hits_indices_

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. 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 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

◆ FLASHTnTAlgorithm() [1/3]

FLASHTnTAlgorithm ( )

constructor

◆ ~FLASHTnTAlgorithm()

~FLASHTnTAlgorithm ( )

overridedefault

destructor

◆ FLASHTnTAlgorithm() [2/3]

FLASHTnTAlgorithm ( const FLASHTnTAlgorithm & )

copy constructor

◆ FLASHTnTAlgorithm() [3/3]

FLASHTnTAlgorithm ( FLASHTnTAlgorithm && other )

default

move constructor

Member Function Documentation

◆ areConsistent_()

bool areConsistent_	(	const ProteinHit &	a,
		const ProteinHit &	b,
		double	tol
	)		const

private

◆ getProteoformHitsMatchedBy()

void getProteoformHitsMatchedBy	(	const FLASHHelperClasses::Tag &	tag,
		std::vector< ProteinHit > &	hits
	)		const

◆ getProteoforms()

void getProteoforms ( std::vector< ProteinHit > & hits ) const

inline

Referenced by TOPPFLASHTnT::main_().

◆ getTags()

void getTags ( std::vector< FLASHHelperClasses::Tag > & tags ) const

◆ markRepresentativeProteoformHits_()

void markRepresentativeProteoformHits_ ( double tol )

private

◆ operator=()

FLASHTnTAlgorithm& operator= ( const FLASHTnTAlgorithm & other )

assignment operator

◆ run()

void run	(	const MSExperiment &	map,
		const std::vector< FASTAFile::FASTAEntry > &	fasta_entry
	)

Find sequence tags from mzs and intensities then store them in tags.

Decoy or MS level 1 spectra are removed by this process. Overlapping PeakGroups in merged spectra are also removed.

Parameters

map	spectra deconvolved by FLASHDeconv.
fasta_entry	fasta entry to searched against

Referenced by TOPPFLASHTnT::main_().

◆ setDefaultParams_()

void setDefaultParams_ ( )

protected

implemented for DefaultParamHandler

◆ 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

◆ decoy_factor_

double decoy_factor_ = 0

private

◆ extender_param_

Param extender_param_

private

◆ keep_decoy_

bool keep_decoy_ = false

private

◆ keep_underdetermined_

bool keep_underdetermined_ = true

private

◆ matching_hits_indices_

std::map<int, std::vector<int> > matching_hits_indices_

private

◆ multiple_hits_per_spec_

bool multiple_hits_per_spec_ = false

private

◆ pro_fdr_

double pro_fdr_ = 1

private

◆ proteoform_hits_

std::vector<ProteinHit> proteoform_hits_

private

◆ prsm_fdr_

double prsm_fdr_ = 1

private

◆ tagger_param_

Param tagger_param_

private

◆ tags_

std::vector<FLASHHelperClasses::Tag> tags_

private

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ FLASHTnTAlgorithm() [1/3]

◆ ~FLASHTnTAlgorithm()

◆ FLASHTnTAlgorithm() [2/3]

◆ FLASHTnTAlgorithm() [3/3]

Member Function Documentation

◆ areConsistent_()

◆ getProteoformHitsMatchedBy()

◆ getProteoforms()

◆ getTags()

◆ markRepresentativeProteoformHits_()

◆ operator=()

◆ run()

◆ setDefaultParams_()

◆ updateMembers_()

Member Data Documentation

◆ decoy_factor_

◆ extender_param_

◆ keep_decoy_

◆ keep_underdetermined_

◆ matching_hits_indices_

◆ multiple_hits_per_spec_

◆ pro_fdr_

◆ proteoform_hits_

◆ prsm_fdr_

◆ tagger_param_

◆ tags_