run with CompNovoIdentificationBase More...

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

Inheritance diagram for CompNovoIdentificationBase:

Collaboration diagram for CompNovoIdentificationBase:

Classes
class	Permut
	Simple class to store permutations and a score. More...

Public Member Functions
constructors and destructors
	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::IonScore	IonScore

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< 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_

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

virtual void	getIdentifications (std::vector< PeptideIdentification > &ids, const PeakMap &exp)=0
	performs an ProteinIdentification run on a PeakMap More...

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

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...

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	getETDSpectrum_ (PeakSpectrum &spec, const String &sequence, Size, double prefix=0.0, double suffix=0.0)
	fills the spectrum with c and z type ions More...

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

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

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 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 CompNovoIdentificationBase

Member Typedef Documentation

◆ IonScore

typedef CompNovoIonScoringBase::IonScore IonScore

Constructor & Destructor Documentation

◆ CompNovoIdentificationBase() [1/2]

CompNovoIdentificationBase ( )

default constructor

◆ CompNovoIdentificationBase() [2/2]

CompNovoIdentificationBase ( const CompNovoIdentificationBase & source )

copy constructor

◆ ~CompNovoIdentificationBase()

~CompNovoIdentificationBase ( )

override

destructor

Member Function Documentation

◆ compareSpectra_()

double compareSpectra_	(	const PeakSpectrum &	s1,
		const PeakSpectrum &	s2
	)

protected

compares two spectra

◆ countMissedCleavagesTryptic_()

Size countMissedCleavagesTryptic_ ( const String & peptide ) const

protected

◆ filterDecomps_()

void filterDecomps_ ( std::vector< MassDecomposition > & decomps )

protected

filters the decomps by the amino acid frequencies

◆ filterPermuts_()

void filterPermuts_ ( std::set< String > & permut )

protected

filters the permutations

◆ getCIDSpectrum_()

void getCIDSpectrum_	(	PeakSpectrum &	spec,
		const String &	sequence,
		Size	charge,
		double	prefix = `0.0`,
		double	suffix = `0.0`
	)

protected

fills the spectrum with b,y ions, multiple charged variants; if prefix and suffix weights are given, the sequence is treated as tag

◆ getCIDSpectrumLight_()

void getCIDSpectrumLight_	(	PeakSpectrum &	spec,
		const String &	sequence,
		double	prefix,
		double	suffix
	)

protected

fills the spec with b and y ions, no other ion types or doubly charged variants are used

◆ getDecompositions_()

void getDecompositions_	(	std::vector< MassDecomposition > &	decomps,
		double	mass,
		bool	no_caching = `false`
	)

protected

produces mass decompositions using the given mass

◆ getETDSpectrum_()

void getETDSpectrum_	(	PeakSpectrum &	spec,
		const String &	sequence,
		Size	,
		double	prefix = `0.0`,
		double	suffix = `0.0`
	)

protected

fills the spectrum with c and z type ions

◆ getIdentifications()

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

pure virtual

performs an ProteinIdentification run on a PeakMap

Implemented in CompNovoIdentificationCID, and CompNovoIdentification.

◆ getModifiedAASequence_()

AASequence getModifiedAASequence_ ( const String & sequence )

protected

returns a modified AASequence from a given internal representation

◆ getModifiedStringFromAASequence_()

String getModifiedStringFromAASequence_ ( const AASequence & sequence )

protected

returns the internal representation of a given AASequence

◆ initIsotopeDistributions_()

void initIsotopeDistributions_ ( )

protected

initializes the score distribution pre-calculated for the use in spectrum generation

◆ operator=()

CompNovoIdentificationBase& operator= ( const CompNovoIdentificationBase & source )

assignment operator

◆ permute_()

static void permute_	(	const String &	prefix,
		String	s,
		std::set< String > &	permutations
	)

staticprotected

permutes the String s adds the prefix and stores the results in permutations

◆ selectPivotIons_()

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`
	)

protected

selects pivot ion of the given range using the scores given in CID_nodes

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

update members method from DefaultParamHandler to update the members

Reimplemented from DefaultParamHandler.

Reimplemented in CompNovoIdentificationCID.

◆ windowMower_()

void windowMower_	(	PeakSpectrum &	spec,
		double	windowsize,
		Size	no_peaks
	)

protected

keep for each window of size windowsize in the m/z range of the spectrum exactly no_peaks

Member Data Documentation

◆ aa_to_weight_

Map<char, double> aa_to_weight_

protected

masses of the amino acids

◆ decomp_cache_

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

protected

◆ decomp_weights_precision_

double decomp_weights_precision_

protected

◆ fragment_mass_tolerance_

double fragment_mass_tolerance_

protected

◆ isotope_distributions_

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

private

◆ mass_decomp_algorithm_

MassDecompositionAlgorithm mass_decomp_algorithm_

protected

◆ max_decomp_weight_

double max_decomp_weight_

protected

◆ max_isotope_

Size max_isotope_

protected

◆ max_mz_

double max_mz_

protected

◆ max_number_aa_per_decomp_

Size max_number_aa_per_decomp_

protected

◆ max_number_pivot_

Size max_number_pivot_

protected

◆ max_subscore_number_

Size max_subscore_number_

protected

◆ min_aa_weight_

double min_aa_weight_ {}

protected

◆ min_mz_

double min_mz_

protected

◆ name_to_residue_

Map<char, const Residue *> name_to_residue_

protected

mapping for the internal representation character to the actual residue

◆ permute_cache_

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

protected

◆ residue_to_name_

Map<const Residue *, char> residue_to_name_

protected

mapping of the actual residue to the internal representing character

◆ subspec_to_sequences_

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

protected

◆ tryptic_only_

bool tryptic_only_

protected

◆ zhang_

ZhangSimilarityScore zhang_

protected

Classes

Public Member Functions

Accessors

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ IonScore

Constructor & Destructor Documentation

◆ CompNovoIdentificationBase() [1/2]

◆ CompNovoIdentificationBase() [2/2]

◆ ~CompNovoIdentificationBase()

Member Function Documentation

◆ compareSpectra_()

◆ countMissedCleavagesTryptic_()

◆ filterDecomps_()

◆ filterPermuts_()

◆ getCIDSpectrum_()

◆ getCIDSpectrumLight_()

◆ getDecompositions_()

◆ getETDSpectrum_()

◆ getIdentifications()

◆ getModifiedAASequence_()

◆ getModifiedStringFromAASequence_()

◆ initIsotopeDistributions_()

◆ operator=()

◆ permute_()

◆ selectPivotIons_()

◆ updateMembers_()

◆ windowMower_()

Member Data Documentation

◆ aa_to_weight_

◆ decomp_cache_

◆ decomp_weights_precision_

◆ fragment_mass_tolerance_

◆ isotope_distributions_

◆ mass_decomp_algorithm_

◆ max_decomp_weight_

◆ max_isotope_

◆ max_mz_

◆ max_number_aa_per_decomp_

◆ max_number_pivot_

◆ max_subscore_number_

◆ min_aa_weight_

◆ min_mz_

◆ name_to_residue_

◆ permute_cache_

◆ residue_to_name_

◆ subspec_to_sequences_

◆ tryptic_only_

◆ zhang_