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

Inheritance diagram for FLASHExtenderAlgorithm:

Collaboration diagram for FLASHExtenderAlgorithm:

Classes
struct	HitInformation

Public Member Functions
	FLASHExtenderAlgorithm ()
	constructor More...

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

	FLASHExtenderAlgorithm (const FLASHExtenderAlgorithm &)=default
	copy constructor More...

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

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

void	run (std::vector< ProteinHit > &hits, const std::vector< FLASHHelperClasses::Tag > &tags, const DeconvolvedSpectrum &dspec, const MSSpectrum &spec, double ppm, bool multiple_hits_per_spec)

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

bool	hasProteoforms () const

void	setModificationMap (const std::map< double, std::vector< ResidueModification >> &mod_map)

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...

Static Public Attributes
static const int	multi_ion_score = 1

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
void	calculatePrecursorMass_ (const ProteinHit &hit, const std::map< int, std::vector< Size >> &best_path_map, HitInformation &hi)

void	defineNodes_ (const DeconvolvedSpectrum &dspec, HitInformation &hi, double max_mass)

void	run_ (const ProteinHit &hit, HitInformation &hi, const std::vector< FLASHHelperClasses::Tag > &matched_tags, std::map< int, std::vector< Size >> &all_paths_per_mode, int max_mod_cntr_for_last_mode)

Size	getVertex_ (int node_index, int pro_index, int score, int num_mod, Size pro_mass_size) const

int	getNodeIndex_ (Size vertex, Size pro_mass_size) const

int	getProIndex_ (Size vertex, Size pro_mass_size) const

int	getModNumber_ (Size vertex) const

int	getScore_ (Size vertex) const

void	constructDAG_ (std::set< Size > &sinks, HitInformation &hi, const std::vector< std::vector< int >> &tag_edges, int max_mod_cntr_for_last_mode, bool use_tags)

void	connectBetweenTags_ (std::set< Size > &visited_tag_edges, HitInformation &hi, std::map< Size, std::tuple< double, double >> &sinks, Size vertex, double truncation_mass, double cumulative_shift, std::map< Size, std::map< int, int >> &node_max_score_map, const std::vector< std::vector< int >> &tag_edges, int max_mod_cntr_for_last_mode, bool use_tags)

void	extendBetweenTags_ (std::map< Size, std::tuple< double, double >> &sinks, HitInformation &hi, Size start_vertex, int end_node_index, int end_pro_index, int diagonal_counter, double truncation_mass, double cumulative_mod_mass, std::map< Size, std::map< int, int >> &node_max_score_map, int max_mod_cntr_for_last_mode)

int	getProteinLength_ (const std::vector< Size > &path, const std::vector< double > &pro_masses) const

double	getSpecMassSpan_ (const std::vector< Size > &path, const MSSpectrum &node_spec, int pro_mass_size) const

double	getProteinMassSpan_ (const std::vector< Size > &path, const std::vector< double > &pro_masses) const

int	getModifiedAACount_ (const std::vector< Size > &path) const

Static Private Member Functions
static void	getProMasses_ (const ProteinHit &hit, std::vector< double > &pro_masses, int mode)

Private Attributes
std::map< double, std::vector< ResidueModification > >	mod_map_

std::vector< std::string >	ion_types_str_

std::vector< double >	prefix_shifts_

std::vector< double >	suffix_shifts_

std::vector< ProteinHit >	proteoform_hits_

std::vector< FLASHHelperClasses::Tag >	tags_

double	tol_

int	max_mod_cntr_ = 0

std::vector< int >	start_pro_indices_

const int	max_path_score_ = 1200

const int	min_path_score_ = -20

const int	max_extension_stretch_ = 50

double	max_mod_mass_ = 500.0

double	given_precursor_mass_ = -1

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_

Class Documentation

◆ OpenMS::FLASHExtenderAlgorithm::HitInformation

struct OpenMS::FLASHExtenderAlgorithm::HitInformation

Collaboration diagram for FLASHExtenderAlgorithm::HitInformation:

[legend]

Class Members
double	calculated_precursor_mass_
DAG	dag_
int	mode_
map< int, MSSpectrum >	node_spec_map_
map< int, vector< double > >	pro_mass_map_
int	protein_end_position_
int	protein_start_position_
map< int, MSSpectrum >	tol_spec_map_
dynamic_bitset	visited_

Constructor & Destructor Documentation

◆ FLASHExtenderAlgorithm() [1/3]

FLASHExtenderAlgorithm ( )

constructor

◆ ~FLASHExtenderAlgorithm()

~FLASHExtenderAlgorithm ( )

overridedefault

destructor

◆ FLASHExtenderAlgorithm() [2/3]

FLASHExtenderAlgorithm ( const FLASHExtenderAlgorithm & )

default

copy constructor

◆ FLASHExtenderAlgorithm() [3/3]

FLASHExtenderAlgorithm ( FLASHExtenderAlgorithm && other )

default

move constructor

Member Function Documentation

◆ calculatePrecursorMass_()

void calculatePrecursorMass_	(	const ProteinHit &	hit,
		const std::map< int, std::vector< Size >> &	best_path_map,
		HitInformation &	hi
	)

private

◆ connectBetweenTags_()

void connectBetweenTags_	(	std::set< Size > &	visited_tag_edges,
		HitInformation &	hi,
		std::map< Size, std::tuple< double, double >> &	sinks,
		Size	vertex,
		double	truncation_mass,
		double	cumulative_shift,
		std::map< Size, std::map< int, int >> &	node_max_score_map,
		const std::vector< std::vector< int >> &	tag_edges,
		int	max_mod_cntr_for_last_mode,
		bool	use_tags
	)

private

◆ constructDAG_()

void constructDAG_	(	std::set< Size > &	sinks,
		HitInformation &	hi,
		const std::vector< std::vector< int >> &	tag_edges,
		int	max_mod_cntr_for_last_mode,
		bool	use_tags
	)

private

◆ defineNodes_()

void defineNodes_	(	const DeconvolvedSpectrum &	dspec,
		HitInformation &	hi,
		double	max_mass
	)

private

◆ extendBetweenTags_()

void extendBetweenTags_	(	std::map< Size, std::tuple< double, double >> &	sinks,
		HitInformation &	hi,
		Size	start_vertex,
		int	end_node_index,
		int	end_pro_index,
		int	diagonal_counter,
		double	truncation_mass,
		double	cumulative_mod_mass,
		std::map< Size, std::map< int, int >> &	node_max_score_map,
		int	max_mod_cntr_for_last_mode
	)

private

◆ getModifiedAACount_()

int getModifiedAACount_ ( const std::vector< Size > & path ) const

private

◆ getModNumber_()

int getModNumber_ ( Size vertex ) const

private

◆ getNodeIndex_()

int getNodeIndex_	(	Size	vertex,
		Size	pro_mass_size
	)		const

private

◆ getProIndex_()

int getProIndex_	(	Size	vertex,
		Size	pro_mass_size
	)		const

private

◆ getProMasses_()

static void getProMasses_	(	const ProteinHit &	hit,
		std::vector< double > &	pro_masses,
		int	mode
	)

staticprivate

◆ getProteinLength_()

int getProteinLength_	(	const std::vector< Size > &	path,
		const std::vector< double > &	pro_masses
	)		const

private

◆ getProteinMassSpan_()

double getProteinMassSpan_	(	const std::vector< Size > &	path,
		const std::vector< double > &	pro_masses
	)		const

private

◆ getProteoforms()

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

inline

◆ getScore_()

int getScore_ ( Size vertex ) const

private

◆ getSpecMassSpan_()

double getSpecMassSpan_	(	const std::vector< Size > &	path,
		const MSSpectrum &	node_spec,
		int	pro_mass_size
	)		const

private

◆ getVertex_()

Size getVertex_	(	int	node_index,
		int	pro_index,
		int	score,
		int	num_mod,
		Size	pro_mass_size
	)		const

private

◆ hasProteoforms()

bool hasProteoforms ( ) const

inline

◆ operator=()

FLASHExtenderAlgorithm& operator= ( const FLASHExtenderAlgorithm & other )

assignment operator

◆ run()

void run	(	std::vector< ProteinHit > &	hits,
		const std::vector< FLASHHelperClasses::Tag > &	tags,
		const DeconvolvedSpectrum &	dspec,
		const MSSpectrum &	spec,
		double	ppm,
		bool	multiple_hits_per_spec
	)

◆ run_()

void run_	(	const ProteinHit &	hit,
		HitInformation &	hi,
		const std::vector< FLASHHelperClasses::Tag > &	matched_tags,
		std::map< int, std::vector< Size >> &	all_paths_per_mode,
		int	max_mod_cntr_for_last_mode
	)

private

◆ setDefaultParams_()

void setDefaultParams_ ( )

protected

implemented for DefaultParamHandler

◆ setModificationMap()

void setModificationMap ( const std::map< double, std::vector< ResidueModification >> & mod_map )

inline

◆ 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

◆ given_precursor_mass_

double given_precursor_mass_ = -1

private

◆ ion_types_str_

std::vector<std::string> ion_types_str_

private

◆ max_extension_stretch_

const int max_extension_stretch_ = 50

private

◆ max_mod_cntr_

int max_mod_cntr_ = 0

private

◆ max_mod_mass_

double max_mod_mass_ = 500.0

private

◆ max_path_score_

const int max_path_score_ = 1200

private

◆ min_path_score_

const int min_path_score_ = -20

private

◆ mod_map_

std::map<double, std::vector<ResidueModification> > mod_map_

private

◆ multi_ion_score

const int multi_ion_score = 1

static

◆ prefix_shifts_

std::vector<double> prefix_shifts_

private

◆ proteoform_hits_

std::vector<ProteinHit> proteoform_hits_

private

◆ start_pro_indices_

std::vector<int> start_pro_indices_

private

◆ suffix_shifts_

std::vector<double> suffix_shifts_

private

◆ tags_

std::vector<FLASHHelperClasses::Tag> tags_

private

◆ tol_

double tol_

private

Classes

Public Member Functions

Static Public Attributes

Protected Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Class Documentation

◆ OpenMS::FLASHExtenderAlgorithm::HitInformation

Constructor & Destructor Documentation

◆ FLASHExtenderAlgorithm() [1/3]

◆ ~FLASHExtenderAlgorithm()

◆ FLASHExtenderAlgorithm() [2/3]

◆ FLASHExtenderAlgorithm() [3/3]

Member Function Documentation

◆ calculatePrecursorMass_()

◆ connectBetweenTags_()

◆ constructDAG_()

◆ defineNodes_()

◆ extendBetweenTags_()

◆ getModifiedAACount_()

◆ getModNumber_()

◆ getNodeIndex_()

◆ getProIndex_()

◆ getProMasses_()

◆ getProteinLength_()

◆ getProteinMassSpan_()

◆ getProteoforms()

◆ getScore_()

◆ getSpecMassSpan_()

◆ getVertex_()

◆ hasProteoforms()

◆ operator=()

◆ run()

◆ run_()

◆ setDefaultParams_()

◆ setModificationMap()

◆ updateMembers_()

Member Data Documentation

◆ given_precursor_mass_

◆ ion_types_str_

◆ max_extension_stretch_

◆ max_mod_cntr_

◆ max_mod_mass_

◆ max_path_score_

◆ min_path_score_

◆ mod_map_

◆ multi_ion_score

◆ prefix_shifts_

◆ proteoform_hits_

◆ start_pro_indices_

◆ suffix_shifts_

◆ tags_

◆ tol_