run with CompNovoIdentificationBase More...

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

Inheritance diagram for CompNovoIdentificationBase:

Classes
class	Permut
	Simple class to store permutations and a score. More...
Public Types
typedef CompNovoIonScoringBase::IonScore	IonScore
Public Member Functions
CompNovoIdentificationBase &	operator= (const CompNovoIdentificationBase &source)
	assignment operator
constructors and destructors

	CompNovoIdentificationBase ()
	default constructor
	CompNovoIdentificationBase (const CompNovoIdentificationBase &source)
	copy constructor
virtual	~CompNovoIdentificationBase ()
	destructor
Accessors

virtual void	getIdentifications (std::vector< PeptideIdentification > &ids, const PeakMap &exp)=0
	performs an ProteinIdentification run on a PeakMap
Protected Member Functions
void	updateMembers_ ()
	update members method from DefaultParamHandler to update the members
void	filterPermuts_ (std::set< String > &permut)
	filters the permutations
void	selectPivotIons_ (std::vector< Size > &pivots, Size left, Size right, Map< DoubleReal, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec, DoubleReal precursor_weight, bool full_range=false)
	selects pivot ion of the given range using the scores given in CID_nodes
void	filterDecomps_ (std::vector< MassDecomposition > &decomps)
	filters the decomps by the amino acid frequencies
void	getDecompositions_ (std::vector< MassDecomposition > &decomps, DoubleReal mass, bool no_caching=false)
	produces mass decompositions using the given mass
void	permute_ (String prefix, String s, std::set< String > &permutations)
	permuts the String s adds the prefix and stores the results in permutations
Size	countMissedCleavagesTryptic_ (const String &peptide) const
void	getCIDSpectrumLight_ (PeakSpectrum &spec, const String &sequence, DoubleReal prefix, DoubleReal suffix)
	fills the spec with b and y ions, no other ion types or doubly charged variants are used
void	getCIDSpectrum_ (PeakSpectrum &spec, const String &sequence, Size charge, DoubleReal prefix=0.0, DoubleReal 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
void	initIsotopeDistributions_ ()
	initializes the score distribution precalculated for the use in spectrum generation
DoubleReal	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
void	windowMower_ (PeakSpectrum &spec, DoubleReal windowsize, Size no_peaks)
	keep for each window of size windowsize in the m/z range of the spectrum exactly no_peaks
DoubleReal	compareSpectra_ (const PeakSpectrum &s1, const PeakSpectrum &s2)
	compares two spectra
AASequence	getModifiedAASequence_ (const String &sequence)
	returns a modified AASequence from a given internal representation
String	getModifiedStringFromAASequence_ (const AASequence &sequence)
	returns the internal representation of a given AASequence
Protected Attributes
Map< char, const Residue * >	name_to_residue_
	mapping for the internal representation character to the actual residue
Map< const Residue *, char >	residue_to_name_
	mapping of the actual residue to the internal representing character
Map< Size, std::vector < DoubleReal > >	isotope_distributions_
Map< char, DoubleReal >	aa_to_weight_
	masses of the amino acids
MassDecompositionAlgorithm	mass_decomp_algorithm_
DoubleReal	min_aa_weight_
ZhangSimilarityScore	zhang_
Map< Size, Map< Size, std::set < String > > >	subspec_to_sequences_
Size	max_number_aa_per_decomp_
bool	tryptic_only_
DoubleReal	fragment_mass_tolerance_
Size	max_number_pivot_
DoubleReal	decomp_weights_precision_
DoubleReal	max_mz_
DoubleReal	min_mz_
DoubleReal	max_decomp_weight_
Size	max_subscore_number_
Size	max_isotope_
Map< DoubleReal, std::vector < MassDecomposition > >	decomp_cache_
Map< String, std::set< String > >	permute_cache_

Detailed Description

run with CompNovoIdentificationBase

Member Typedef Documentation

typedef CompNovoIonScoringBase::IonScore IonScore

Reimplemented in CompNovoIdentification, and CompNovoIdentificationCID.

Constructor & Destructor Documentation

CompNovoIdentificationBase ( )

default constructor

CompNovoIdentificationBase ( const CompNovoIdentificationBase & source )

copy constructor

virtual ~CompNovoIdentificationBase ( ) [virtual]

destructor

Member Function Documentation

DoubleReal compareSpectra_	(	const PeakSpectrum &	s1,
		const PeakSpectrum &	s2
	)			`[protected]`

compares two spectra

Size countMissedCleavagesTryptic_ ( const String & peptide ) const [protected]

DoubleReal estimatePrecursorWeight_	(	const PeakSpectrum &	ETD_spec,
		Size &	charge
	)			`[protected]`

estimates an exact precursor weight of the ETD spectrum, because in most of the cases the precursor is found in the MS/MS spec

Reimplemented in CompNovoIdentification.

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

filters the decomps by the amino acid frequencies

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

filters the permutations

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

void getCIDSpectrumLight_	(	PeakSpectrum &	spec,
		const String &	sequence,
		DoubleReal	prefix,
		DoubleReal	suffix
	)			`[protected]`

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

void getDecompositions_	(	std::vector< MassDecomposition > &	decomps,
		DoubleReal	mass,
		bool	no_caching = `false`
	)			`[protected]`

produces mass decompositions using the given mass

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

performs an ProteinIdentification run on a PeakMap

Implemented in CompNovoIdentification, and CompNovoIdentificationCID.

AASequence getModifiedAASequence_ ( const String & sequence ) [protected]

returns a modified AASequence from a given internal representation

String getModifiedStringFromAASequence_ ( const AASequence & sequence ) [protected]

returns the internal representation of a given AASequence

void initIsotopeDistributions_ ( ) [protected]

initializes the score distribution precalculated for the use in spectrum generation

CompNovoIdentificationBase& operator= ( const CompNovoIdentificationBase & source )

assignment operator

void permute_	(	String	prefix,
		String	s,
		std::set< String > &	permutations
	)			`[protected]`

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

void selectPivotIons_	(	std::vector< Size > &	pivots,
		Size	left,
		Size	right,
		Map< DoubleReal, IonScore > &	CID_nodes,
		const PeakSpectrum &	CID_orig_spec,
		DoubleReal	precursor_weight,
		bool	full_range = `false`
	)			`[protected]`