This class implements the database preprocessing needing for precursor ion selection. More...

#include <OpenMS/ANALYSIS/TARGETED/PrecursorIonSelectionPreprocessing.h>

Inheritance diagram for PrecursorIonSelectionPreprocessing:

Collaboration diagram for PrecursorIonSelectionPreprocessing:

Public Member Functions
	PrecursorIonSelectionPreprocessing ()

	PrecursorIonSelectionPreprocessing (const PrecursorIonSelectionPreprocessing &source)

	~PrecursorIonSelectionPreprocessing () override

PrecursorIonSelectionPreprocessing &	operator= (const PrecursorIonSelectionPreprocessing &source)

const std::map< String, std::vector< double > > &	getProtMasses () const

const std::vector< double > &	getMasses (String acc) const

const std::map< String, std::vector< double > > &	getProteinRTMap () const

const std::map< String, std::vector< double > > &	getProteinPTMap () const

const std::map< String, std::vector< String > > &	getProteinPeptideSequenceMap () const

void	dbPreprocessing (String db_path, bool save=true)
	Calculates tryptic peptide masses of a given database and stores masses and peptide sequences. More...

void	dbPreprocessing (String db_path, String rt_model_path, String dt_model_path, bool save=true)
	Calculates tryptic peptide masses of a given database and stores masses and peptide sequences. More...

void	loadPreprocessing ()
	Loads tryptic peptide masses of a given database. More...

double	getWeight (double mass)
	get the weighted frequency of a mass More...

double	getRT (String prot_id, Size peptide_index)

double	getPT (String prot_id, Size peptide_index)

void	setFixedModifications (StringList &modifications)

const std::map< char, std::vector< String > > &	getFixedModifications ()

void	setGaussianParameters (double mu, double sigma)

double	getGaussMu ()

double	getGaussSigma ()

double	getRTProbability (String prot_id, Size peptide_index, Feature &feature)

double	getRTProbability (double pred_rt, Feature &feature)

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	savePreprocessedDB_ (String db_path, String path)
	saves the preprocessed db More...

void	savePreprocessedDBWithRT_ (String db_path, String path)

void	loadPreprocessedDB_ (String path)
	loads the preprocessed db More...

void	filterTaxonomyIdentifier_ (FASTAFile::FASTAEntry &entry)
	pre-process fasta identifier More...

Int	getScanNumber_ (double rt)

double	getRTProbability_ (double min_obs_rt, double max_obs_rt, double pred_rt)

void	updateMembers_ () override
	update members method from DefaultParamHandler to update the members More...

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

Protected Attributes
std::vector< double >	masses_
	all tryptic masses of the distinct peptides in the database More...

std::set< AASequence >	sequences_
	the sequences of the tryptic peptides More...

std::map< String, std::vector< double > >	prot_masses_
	stores masses of tryptic peptides for proteins, key is the accession number More...

std::vector< double >	bin_masses_
	the masses of the bins used for preprocessing (only used if bins are not equidistant, i.e. with ppm) More...

std::vector< UInt >	counter_
	counter for the bins More...

UInt	f_max_
	maximal relative frequency of a mass More...

bool	fixed_mods_

std::map< String, std::vector< double > >	rt_prot_map_

std::map< String, std::vector< double > >	pt_prot_map_

std::map< String, std::vector< String > >	prot_peptide_seq_map_

std::map< char, std::vector< String > >	fixed_modifications_

double	sigma_

double	mu_

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...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
	Writes all parameters to meta values. More...

Detailed Description

This class implements the database preprocessing needing for precursor ion selection.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
precursor_mass_tolerance	float	10.0	min: 0.0	Precursor mass tolerance which is used to query the peptide database for peptides
precursor_mass_tolerance_unit	string	ppm	ppm, Da	Precursor mass tolerance unit.
preprocessed_db_path	string			Path where the preprocessed database should be stored
preprocessed_db_pred_rt_path	string			Path where the predicted rts of the preprocessed database should be stored
preprocessed_db_pred_dt_path	string			Path where the predicted rts of the preprocessed database should be stored
max_peptides_per_run	int	100000	min: 1	Number of peptides for that the pt and rt are parallely predicted.
missed_cleavages	int	1	min: 0	Number of allowed missed cleavages.
taxonomy	string			Taxonomy
tmp_dir	string			Absolute path to tmp data directory used to store files needed for rt and dt prediction.
store_peptide_sequences	string	false		Flag if peptide sequences should be stored.
rt_settings:min_rt	float	960.0	min: 1.0	Minimal RT in the experiment (in seconds)
rt_settings:max_rt	float	3840.0		Maximal RT in the experiment (in seconds)
rt_settings:rt_step_size	float	30.0		Time between two consecutive spectra (in seconds)
rt_settings:gauss_mean	float	-1.0		mean of the gauss curve
rt_settings:gauss_sigma	float	3.0		std of the gauss curve

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Constructor & Destructor Documentation

◆ PrecursorIonSelectionPreprocessing() [1/2]

PrecursorIonSelectionPreprocessing ( )

◆ PrecursorIonSelectionPreprocessing() [2/2]

PrecursorIonSelectionPreprocessing ( const PrecursorIonSelectionPreprocessing & source )

◆ ~PrecursorIonSelectionPreprocessing()

~PrecursorIonSelectionPreprocessing ( )

override

Member Function Documentation

◆ dbPreprocessing() [1/2]

void dbPreprocessing	(	String	db_path,
		bool	save = `true`
	)

Calculates tryptic peptide masses of a given database and stores masses and peptide sequences.

Parameters

db_path	Path to database file (fasta)
save	Flag if preprocessing should be stored.

Exceptions

Exception::FileNotFound	if file with preprocessing or db can't be found
Exception::UnableToCreateFile	if preprocessing file can't be written

◆ dbPreprocessing() [2/2]

void dbPreprocessing	(	String	db_path,
		String	rt_model_path,
		String	dt_model_path,
		bool	save = `true`
	)

Calculates tryptic peptide masses of a given database and stores masses and peptide sequences.

Parameters

db_path	Path to database file (fasta)
rt_model_path
dt_model_path
save	Flag if preprocessing should be stored.

Exceptions

Exception::FileNotFound	if file with preprocessing or db can't be found
Exception::UnableToCreateFile	if preprocessing file can't be written

◆ filterTaxonomyIdentifier_()

void filterTaxonomyIdentifier_ ( FASTAFile::FASTAEntry & entry )

protected

pre-process fasta identifier

◆ getFixedModifications()

const std::map<char, std::vector<String> >& getFixedModifications ( )

inline

◆ getGaussMu()

double getGaussMu ( )

inline

◆ getGaussSigma()

double getGaussSigma ( )

inline

◆ getMasses()

const std::vector<double>& getMasses ( String acc ) const

◆ getProteinPeptideSequenceMap()

const std::map<String, std::vector<String> >& getProteinPeptideSequenceMap ( ) const

◆ getProteinPTMap()

const std::map<String, std::vector<double> >& getProteinPTMap ( ) const

◆ getProteinRTMap()

const std::map<String, std::vector<double> >& getProteinRTMap ( ) const

◆ getProtMasses()

const std::map<String, std::vector<double> >& getProtMasses ( ) const

◆ getPT()

double getPT	(	String	prot_id,
		Size	peptide_index
	)

◆ getRT()

double getRT	(	String	prot_id,
		Size	peptide_index
	)

◆ getRTProbability() [1/2]

double getRTProbability	(	double	pred_rt,
		Feature &	feature
	)

◆ getRTProbability() [2/2]

double getRTProbability	(	String	prot_id,
		Size	peptide_index,
		Feature &	feature
	)

◆ getRTProbability_()

double getRTProbability_	(	double	min_obs_rt,
		double	max_obs_rt,
		double	pred_rt
	)

protected

◆ getScanNumber_()

Int getScanNumber_ ( double rt )

protected

◆ getWeight()

double getWeight ( double mass )

get the weighted frequency of a mass

◆ loadPreprocessedDB_()

void loadPreprocessedDB_ ( String path )

protected

loads the preprocessed db

◆ loadPreprocessing()

void loadPreprocessing ( )

Loads tryptic peptide masses of a given database.

Exceptions

Exception::FileNotFound	if file with preprocessing can't be found
Exception::InvalidParameter	if precursor_mass_tolerance_unit is ppm and file containing bin borders can't be found

◆ operator=()

PrecursorIonSelectionPreprocessing& operator= ( const PrecursorIonSelectionPreprocessing & source )

◆ savePreprocessedDB_()

void savePreprocessedDB_	(	String	db_path,
		String	path
	)

protected

saves the preprocessed db

◆ savePreprocessedDBWithRT_()

void savePreprocessedDBWithRT_	(	String	db_path,
		String	path
	)

protected

◆ setFixedModifications()

void setFixedModifications ( StringList & modifications )

◆ setGaussianParameters()

void setGaussianParameters	(	double	mu,
		double	sigma
	)

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

update members method from DefaultParamHandler to update the members

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ bin_masses_

std::vector<double> bin_masses_

protected

the masses of the bins used for preprocessing (only used if bins are not equidistant, i.e. with ppm)

◆ counter_

std::vector<UInt> counter_

protected

counter for the bins

◆ f_max_

UInt f_max_

protected

maximal relative frequency of a mass

◆ fixed_modifications_

std::map<char, std::vector<String> > fixed_modifications_

protected

◆ fixed_mods_

bool fixed_mods_

protected

◆ masses_

std::vector<double> masses_

protected

all tryptic masses of the distinct peptides in the database

◆ mu_

double mu_

protected

◆ prot_masses_

std::map<String, std::vector<double> > prot_masses_

protected

stores masses of tryptic peptides for proteins, key is the accession number

◆ prot_peptide_seq_map_

std::map<String, std::vector<String> > prot_peptide_seq_map_

protected

◆ pt_prot_map_

std::map<String, std::vector<double> > pt_prot_map_

protected

◆ rt_prot_map_

std::map<String, std::vector<double> > rt_prot_map_

protected

◆ sequences_

std::set<AASequence> sequences_

protected

the sequences of the tryptic peptides

◆ sigma_

double sigma_

protected

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PrecursorIonSelectionPreprocessing() [1/2]

◆ PrecursorIonSelectionPreprocessing() [2/2]

◆ ~PrecursorIonSelectionPreprocessing()

Member Function Documentation

◆ dbPreprocessing() [1/2]

◆ dbPreprocessing() [2/2]

◆ filterTaxonomyIdentifier_()

◆ getFixedModifications()

◆ getGaussMu()

◆ getGaussSigma()

◆ getMasses()

◆ getProteinPeptideSequenceMap()

◆ getProteinPTMap()

◆ getProteinRTMap()

◆ getProtMasses()

◆ getPT()

◆ getRT()

◆ getRTProbability() [1/2]

◆ getRTProbability() [2/2]

◆ getRTProbability_()

◆ getScanNumber_()

◆ getWeight()

◆ loadPreprocessedDB_()

◆ loadPreprocessing()

◆ operator=()

◆ savePreprocessedDB_()

◆ savePreprocessedDBWithRT_()

◆ setFixedModifications()

◆ setGaussianParameters()

◆ updateMembers_()

Member Data Documentation

◆ bin_masses_

◆ counter_

◆ f_max_

◆ fixed_modifications_

◆ fixed_mods_

◆ masses_

◆ mu_

◆ prot_masses_

◆ prot_peptide_seq_map_

◆ pt_prot_map_

◆ rt_prot_map_

◆ sequences_

◆ sigma_