OpenMS
CompNovoIdentificationBase Class Referenceabstract

run with CompNovoIdentificationBase More...

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

Inheritance diagram for CompNovoIdentificationBase:
[legend]
Collaboration diagram for CompNovoIdentificationBase:
[legend]

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...
 
CompNovoIdentificationBaseoperator= (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...
 
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...
 

Accessors

typedef CompNovoIonScoringBase::IonScore IonScore
 
std::map< char, const Residue * > name_to_residue_
 mapping for the internal representation character to the actual residue More...
 
std::map< const Residue *, char > residue_to_name_
 mapping of the actual residue to the internal representing character More...
 
std::map< char, double > aa_to_weight_
 masses of the amino acids More...
 
MassDecompositionAlgorithm mass_decomp_algorithm_
 
double min_aa_weight_ {}
 
ZhangSimilarityScore zhang_
 
std::map< Size, std::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_
 
std::map< double, std::vector< MassDecomposition > > decomp_cache_
 
std::map< String, std::set< String > > permute_cache_
 
std::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) const
 filters the permutations More...
 
void selectPivotIons_ (std::vector< Size > &pivots, Size left, Size right, std::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) const
 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 &key_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< 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

Member Typedef Documentation

◆ IonScore

Constructor & Destructor Documentation

◆ CompNovoIdentificationBase() [1/2]

default constructor

◆ CompNovoIdentificationBase() [2/2]

copy constructor

◆ ~CompNovoIdentificationBase()

destructor

Member Function Documentation

◆ compareSpectra_()

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

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,
std::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_

std::map<char, double> aa_to_weight_
protected

masses of the amino acids

◆ decomp_cache_

std::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_

std::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_

std::map<char, const Residue *> name_to_residue_
protected

mapping for the internal representation character to the actual residue

◆ permute_cache_

std::map<String, std::set<String> > permute_cache_
protected

◆ residue_to_name_

std::map<const Residue *, char> residue_to_name_
protected

mapping of the actual residue to the internal representing character

◆ subspec_to_sequences_

std::map<Size, std::map<Size, std::set<String> > > subspec_to_sequences_
protected

◆ tryptic_only_

bool tryptic_only_
protected

◆ zhang_

ZhangSimilarityScore zhang_
protected