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

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

Inheritance diagram for PrecursorIonSelectionPreprocessing:

Public Member Functions
	PrecursorIonSelectionPreprocessing ()
	PrecursorIonSelectionPreprocessing (const PrecursorIonSelectionPreprocessing &source)
	~PrecursorIonSelectionPreprocessing ()
PrecursorIonSelectionPreprocessing &	operator= (const PrecursorIonSelectionPreprocessing &source)
const std::map< String, std::vector< DoubleReal > > &	getProtMasses () const
const std::vector< DoubleReal > &	getMasses (String acc) const
const std::map< String, std::vector< DoubleReal > > &	getProteinRTMap () const
const std::map< String, std::vector< DoubleReal > > &	getProteinPTMap () const
const std::map< String, std::vector< String > > &	getProteinPeptideSequenceMap () const
void	dbPreprocessing (String db_path, bool save=true)
	Calculates tryptric peptide masses of a given database and stores masses and peptide sequences.
void	dbPreprocessing (String db_path, String rt_model_path, String dt_model_path, bool save=true)
	Calculates tryptric peptide masses of a given database and stores masses and peptide sequences.
void	loadPreprocessing ()
	Loads tryptric peptide masses of a given database.
DoubleReal	getWeight (DoubleReal mass)
	get the weighted frequency of a mass
DoubleReal	getRT (String prot_id, Size peptide_index)
DoubleReal	getPT (String prot_id, Size peptide_index)
void	setFixedModifications (StringList &modifications)
const std::map< char, std::vector< String > > &	getFixedModifications ()
void	setGaussianParameters (DoubleReal mu, DoubleReal sigma)
DoubleReal	getGaussMu ()
DoubleReal	getGaussSigma ()
DoubleReal	getRTProbability (String prot_id, Size peptide_index, Feature &feature)
DoubleReal	getRTProbability (DoubleReal pred_rt, Feature &feature)
Protected Member Functions
void	savePreprocessedDB_ (String db_path, String path)
	saves the preprocessed db
void	savePreprocessedDBWithRT_ (String db_path, String path)
void	loadPreprocessedDB_ (String path)
	loads the preprocessed db
void	filterTaxonomyIdentifier_ (FASTAFile::FASTAEntry &entry)
	preprocess fasta identifier
Int	getScanNumber_ (DoubleReal rt)
DoubleReal	getRTProbability_ (DoubleReal min_obs_rt, DoubleReal max_obs_rt, DoubleReal pred_rt)
void	updateMembers_ ()
	update members method from DefaultParamHandler to update the members
Protected Attributes
std::vector< DoubleReal >	masses_
	all tryptic masses of the distinct peptides in the database
std::set< AASequence >	sequences_
	the sequences of the tryptic peptides
std::map< String, std::vector < DoubleReal > >	prot_masses_
	stores masses of tryptic peptides for proteins, key is the accession number
std::vector< DoubleReal >	bin_masses_
	the masses of the bins used for preprocessing (only used if bins are not equidistant, i.e. with ppm)
std::vector< UInt >	counter_
	counter for the bins
UInt	f_max_
	maximal relative frequency of a mass
bool	fixed_mods_
std::map< String, std::vector < DoubleReal > >	rt_prot_map_
std::map< String, std::vector < DoubleReal > >	pt_prot_map_
std::map< String, std::vector < String > >	prot_peptide_seq_map_
std::map< char, std::vector < String > >	fixed_modifications_
DoubleReal	sigma_
DoubleReal	mu_

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	min: 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	min: 1	Minimal RT in the experiment (in seconds)
rt_settings:max_rt	float	3840		Maximal RT in the experiment (in seconds)
rt_settings:rt_step_size	float	30		Time between two consecutive spectra (in seconds)
rt_settings:gauss_mean	float	-1		mean of the gauss curve
rt_settings:gauss_sigma	float	3		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 ( )

PrecursorIonSelectionPreprocessing ( const PrecursorIonSelectionPreprocessing & source )

~PrecursorIonSelectionPreprocessing ( )

Member Function Documentation

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

Calculates tryptric 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

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

Calculates tryptric 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

void filterTaxonomyIdentifier_ ( FASTAFile::FASTAEntry & entry ) [protected]

preprocess fasta identifier

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

DoubleReal getGaussMu ( ) [inline]

DoubleReal getGaussSigma ( ) [inline]

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

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

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

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

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

DoubleReal getPT	(	String	prot_id,
		Size	peptide_index
	)

DoubleReal getRT	(	String	prot_id,
		Size	peptide_index
	)

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

DoubleReal getRTProbability	(	DoubleReal	pred_rt,
		Feature &	feature
	)

DoubleReal getRTProbability_	(	DoubleReal	min_obs_rt,
		DoubleReal	max_obs_rt,
		DoubleReal	pred_rt
	)			`[protected]`

Int getScanNumber_ ( DoubleReal rt ) [protected]

DoubleReal getWeight ( DoubleReal mass )

get the weighted frequency of a mass

void loadPreprocessedDB_ ( String path ) [protected]

loads the preprocessed db

void loadPreprocessing ( )

Loads tryptric 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

PrecursorIonSelectionPreprocessing& operator= ( const PrecursorIonSelectionPreprocessing & source )

void savePreprocessedDB_	(	String	db_path,
		String	path
	)			`[protected]`

saves the preprocessed db

void savePreprocessedDBWithRT_	(	String	db_path,
		String	path
	)			`[protected]`

void setFixedModifications ( StringList & modifications )

void setGaussianParameters	(	DoubleReal	mu,
		DoubleReal	sigma
	)

void updateMembers_ ( ) [protected, virtual]

update members method from DefaultParamHandler to update the members

Reimplemented from DefaultParamHandler.

Member Data Documentation

std::vector<DoubleReal> bin_masses_ [protected]

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

std::vector<UInt> counter_ [protected]

counter for the bins

UInt f_max_ [protected]

maximal relative frequency of a mass

std::map<char, std::vector<String> > fixed_modifications_ [protected]

bool fixed_mods_ [protected]

std::vector<DoubleReal> masses_ [protected]

all tryptic masses of the distinct peptides in the database

DoubleReal mu_ [protected]

std::map<String, std::vector<DoubleReal> > prot_masses_ [protected]

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

std::map<String, std::vector<String> > prot_peptide_seq_map_ [protected]

std::map<String, std::vector<DoubleReal> > pt_prot_map_ [protected]

std::map<String, std::vector<DoubleReal> > rt_prot_map_ [protected]

std::set<AASequence> sequences_ [protected]

the sequences of the tryptic peptides

DoubleReal sigma_ [protected]

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1

PrecursorIonSelectionPreprocessing Class Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation