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CompNovoIdentificationCID Class Reference

run with CompNovoIdentificationCID More...

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

Inheritance diagram for CompNovoIdentificationCID:
CompNovoIdentificationBase DefaultParamHandler

Public Types

typedef CompNovoIonScoringBase::IsotopeType IsotopeType
 
typedef CompNovoIonScoringBase::IonScore IonScore
 
typedef CompNovoIdentificationBase::Permut Permut
 
- Public Types inherited from CompNovoIdentificationBase
typedef CompNovoIonScoringBase::IonScore IonScore
 

Public Member Functions

CompNovoIdentificationCIDoperator= (const CompNovoIdentificationCID &source)
 
constructors and destructors
 CompNovoIdentificationCID ()
 default constructor More...
 
 CompNovoIdentificationCID (const CompNovoIdentificationCID &source)
 copy constructor More...
 
virtual ~CompNovoIdentificationCID ()
 destructor More...
 
Accessors
void getIdentifications (std::vector< PeptideIdentification > &ids, const PeakMap &exp)
 performs an ProteinIdentification run on a PeakMap More...
 
void getIdentification (PeptideIdentification &id, const PeakSpectrum &CID_spec)
 performs an ProteinIdentification run on a PeakSpectrum More...
 
- Public Member Functions inherited from CompNovoIdentificationBase
CompNovoIdentificationBaseoperator= (const CompNovoIdentificationBase &source)
 assignment operator More...
 
 CompNovoIdentificationBase ()
 default constructor More...
 
 CompNovoIdentificationBase (const CompNovoIdentificationBase &source)
 copy constructor More...
 
virtual ~CompNovoIdentificationBase ()
 destructor 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 DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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 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_ ()
 update members method from DefaultParamHandler to update the members More...
 
- 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

double precursor_mass_tolerance_
 
- 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, doubleaa_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< Stringsubsections_
 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

Constructor & Destructor Documentation

default constructor

copy constructor

virtual ~CompNovoIdentificationCID ( )
virtual

destructor

Member Function Documentation

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

void getIdentification ( PeptideIdentification id,
const PeakSpectrum CID_spec 
)

performs an ProteinIdentification run on a PeakSpectrum

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

performs an ProteinIdentification run on a PeakMap

Implements CompNovoIdentificationBase.

CompNovoIdentificationCID& operator= ( const CompNovoIdentificationCID source)
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

void updateMembers_ ( )
protectedvirtual

update members method from DefaultParamHandler to update the members

Reimplemented from CompNovoIdentificationBase.

Member Data Documentation

double precursor_mass_tolerance_
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 12:49:27 using doxygen 1.8.11