run with CompNovoIdentificationCID More...

#include <OpenMS/ANALYSIS/DENOVO/CompNovoIdentificationCID.h>

Inheritance diagram for CompNovoIdentificationCID:

Public Member Functions
constructors and destructors
	CompNovoIdentificationCID ()
	default constructor More...

	CompNovoIdentificationCID (const CompNovoIdentificationCID &source)
	copy constructor More...

	~CompNovoIdentificationCID () override
	destructor More...

CompNovoIdentificationCID &	operator= (const CompNovoIdentificationCID &source)

Public Member Functions inherited from CompNovoIdentificationBase
	CompNovoIdentificationBase ()
	default constructor More...

	CompNovoIdentificationBase (const CompNovoIdentificationBase &source)
	copy constructor More...

	~CompNovoIdentificationBase () override
	destructor More...

CompNovoIdentificationBase &	operator= (const CompNovoIdentificationBase &source)
	assignment operator 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...

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...

Accessors
typedef CompNovoIonScoringBase::IsotopeType	IsotopeType

typedef CompNovoIonScoringBase::IonScore	IonScore

typedef CompNovoIdentificationBase::Permut	Permut

double	precursor_mass_tolerance_

void	getIdentifications (std::vector< PeptideIdentification > &ids, const PeakMap &exp) override
	performs an ProteinIdentification run on a PeakMap More...

void	getIdentification (PeptideIdentification &id, const PeakSpectrum &CID_spec)
	performs an ProteinIdentification run on a PeakSpectrum More...

void	getDecompositionsDAC_ (std::set< String > &sequences, Size left, Size right, double peptide_weight, const PeakSpectrum &CID_orig_spec, Map< double, IonScore > &CID_nodes)
	call the DAC algorithm for the subspectrum defined via left and right peaks and fill the set with candidates sequences More...

void	reducePermuts_ (std::set< String > &permuts, const PeakSpectrum &CID_orig_spec, double prefix, double suffix)
	reduces the given number of permuts by scoring the permutations to the CID and ETD spec More...

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

Additional Inherited Members
Public Types inherited from CompNovoIdentificationBase
typedef CompNovoIonScoringBase::IonScore	IonScore

Protected Member Functions inherited from CompNovoIdentificationBase
void	filterPermuts_ (std::set< String > &permut)
	filters the permutations More...

void	selectPivotIons_ (std::vector< Size > &pivots, Size left, Size right, Map< double, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec, double precursor_weight, bool full_range=false)
	selects pivot ion of the given range using the scores given in CID_nodes More...

void	filterDecomps_ (std::vector< MassDecomposition > &decomps)
	filters the decomps by the amino acid frequencies More...

void	getDecompositions_ (std::vector< MassDecomposition > &decomps, double mass, bool no_caching=false)
	produces mass decompositions using the given mass More...

void	permute_ (String prefix, String s, std::set< String > &permutations)
	permuts the String s adds the prefix and stores the results in permutations More...

Size	countMissedCleavagesTryptic_ (const String &peptide) const

void	getCIDSpectrumLight_ (PeakSpectrum &spec, const String &sequence, double prefix, double suffix)
	fills the spec with b and y ions, no other ion types or doubly charged variants are used More...

void	getCIDSpectrum_ (PeakSpectrum &spec, const String &sequence, Size charge, double prefix=0.0, double suffix=0.0)
	fills the spectrum with b,y ions, multiple charged variants; if prefix and suffix weights are given, the sequence is treated as tag More...

void	initIsotopeDistributions_ ()
	initializes the score distribution pre-calculated for the use in spectrum generation More...

double	estimatePrecursorWeight_ (const PeakSpectrum &ETD_spec, Size &charge)
	estimates an exact precursor weight of the ETD spectrum, because in most of the cases the precursor is found in the MS/MS spec More...

void	windowMower_ (PeakSpectrum &spec, double windowsize, Size no_peaks)
	keep for each window of size windowsize in the m/z range of the spectrum exactly no_peaks More...

double	compareSpectra_ (const PeakSpectrum &s1, const PeakSpectrum &s2)
	compares two spectra More...

AASequence	getModifiedAASequence_ (const String &sequence)
	returns a modified AASequence from a given internal representation More...

String	getModifiedStringFromAASequence_ (const AASequence &sequence)
	returns the internal representation of a given AASequence More...

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

Protected Attributes inherited from CompNovoIdentificationBase
Map< char, const Residue * >	name_to_residue_
	mapping for the internal representation character to the actual residue More...

Map< const Residue *, char >	residue_to_name_
	mapping of the actual residue to the internal representing character More...

Map< Size, std::vector< double > >	isotope_distributions_

Map< char, double >	aa_to_weight_
	masses of the amino acids More...

MassDecompositionAlgorithm	mass_decomp_algorithm_

double	min_aa_weight_

ZhangSimilarityScore	zhang_

Map< Size, Map< Size, std::set< String > > >	subspec_to_sequences_

Size	max_number_aa_per_decomp_

bool	tryptic_only_

double	fragment_mass_tolerance_

Size	max_number_pivot_

double	decomp_weights_precision_

double	max_mz_

double	min_mz_

double	max_decomp_weight_

Size	max_subscore_number_

Size	max_isotope_

Map< double, std::vector< MassDecomposition > >	decomp_cache_

Map< String, std::set< String > >	permute_cache_

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...

Detailed Description

run with CompNovoIdentificationCID

Member Typedef Documentation

◆ IonScore

typedef CompNovoIonScoringBase::IonScore IonScore

◆ IsotopeType

typedef CompNovoIonScoringBase::IsotopeType IsotopeType

◆ Permut

typedef CompNovoIdentificationBase::Permut Permut

Constructor & Destructor Documentation

◆ CompNovoIdentificationCID() [1/2]

CompNovoIdentificationCID ( )

default constructor

◆ CompNovoIdentificationCID() [2/2]

CompNovoIdentificationCID ( const CompNovoIdentificationCID & source )

copy constructor

◆ ~CompNovoIdentificationCID()

~CompNovoIdentificationCID ( )

override

destructor

Member Function Documentation

◆ getDecompositionsDAC_()

void getDecompositionsDAC_	(	std::set< String > &	sequences,
		Size	left,
		Size	right,
		double	peptide_weight,
		const PeakSpectrum &	CID_orig_spec,
		Map< double, IonScore > &	CID_nodes
	)

protected

call the DAC algorithm for the subspectrum defined via left and right peaks and fill the set with candidates sequences

◆ getIdentification()

void getIdentification	(	PeptideIdentification &	id,
		const PeakSpectrum &	CID_spec
	)

performs an ProteinIdentification run on a PeakSpectrum

◆ getIdentifications()

void getIdentifications	(	std::vector< PeptideIdentification > &	ids,
		const PeakMap &	exp
	)

overridevirtual

performs an ProteinIdentification run on a PeakMap

Implements CompNovoIdentificationBase.

◆ operator=()

CompNovoIdentificationCID& operator= ( const CompNovoIdentificationCID & source )

◆ reducePermuts_()

void reducePermuts_	(	std::set< String > &	permuts,
		const PeakSpectrum &	CID_orig_spec,
		double	prefix,
		double	suffix
	)

protected

reduces the given number of permuts by scoring the permutations to the CID and ETD spec

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

update members method from DefaultParamHandler to update the members

Reimplemented from CompNovoIdentificationBase.

Member Data Documentation

◆ precursor_mass_tolerance_

double precursor_mass_tolerance_

protected

Public Member Functions

Accessors

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ IonScore

◆ IsotopeType

◆ Permut

Constructor & Destructor Documentation

◆ CompNovoIdentificationCID() [1/2]

◆ CompNovoIdentificationCID() [2/2]

◆ ~CompNovoIdentificationCID()

Member Function Documentation

◆ getDecompositionsDAC_()

◆ getIdentification()

◆ getIdentifications()

◆ operator=()

◆ reducePermuts_()

◆ updateMembers_()

Member Data Documentation

◆ precursor_mass_tolerance_