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 More... | |
constructors and destructors | |
| CompNovoIdentificationBase () | |
| default constructor More... | |
| CompNovoIdentificationBase (const CompNovoIdentificationBase &source) | |
| copy constructor More... | |
| virtual | ~CompNovoIdentificationBase () |
| destructor More... | |
Accessors | |
| virtual void | getIdentifications (std::vector< PeptideIdentification > &ids, const PeakMap &exp)=0 |
| performs an ProteinIdentification run on a PeakMap 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 ¶m) |
| 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... | |
Protected Member Functions | |
| void | updateMembers_ () |
| 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... | |
| 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 | |
| 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 CompNovoIdentificationBase
Member Typedef Documentation
◆ IonScore
Constructor & Destructor Documentation
◆ CompNovoIdentificationBase() [1/2]
default constructor
◆ CompNovoIdentificationBase() [2/2]
| CompNovoIdentificationBase | ( | const CompNovoIdentificationBase & | source | ) |
copy constructor
◆ ~CompNovoIdentificationBase()
|
virtual |
destructor
Member Function Documentation
◆ compareSpectra_()
|
protected |
compares two spectra
◆ countMissedCleavagesTryptic_()
◆ estimatePrecursorWeight_()
|
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
◆ filterDecomps_()
|
protected |
filters the decomps by the amino acid frequencies
◆ filterPermuts_()
|
protected |
filters the permutations
◆ getCIDSpectrum_()
|
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_()
|
protected |
fills the spec with b and y ions, no other ion types or doubly charged variants are used
◆ getDecompositions_()
|
protected |
produces mass decompositions using the given mass
◆ getIdentifications()
|
pure virtual |
performs an ProteinIdentification run on a PeakMap
Implemented in CompNovoIdentification, and CompNovoIdentificationCID.
◆ getModifiedAASequence_()
|
protected |
returns a modified AASequence from a given internal representation
◆ getModifiedStringFromAASequence_()
|
protected |
returns the internal representation of a given AASequence
◆ initIsotopeDistributions_()
|
protected |
initializes the score distribution pre-calculated for the use in spectrum generation
◆ operator=()
| CompNovoIdentificationBase& operator= | ( | const CompNovoIdentificationBase & | source | ) |
assignment operator
◆ permute_()
permuts the String s adds the prefix and stores the results in permutations
◆ selectPivotIons_()
|
protected |
selects pivot ion of the given range using the scores given in CID_nodes
◆ updateMembers_()
|
protectedvirtual |
update members method from DefaultParamHandler to update the members
Reimplemented from DefaultParamHandler.
Reimplemented in CompNovoIdentificationCID.
◆ windowMower_()
|
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_
◆ decomp_cache_
|
protected |
◆ decomp_weights_precision_
|
protected |
◆ fragment_mass_tolerance_
|
protected |
◆ isotope_distributions_
◆ mass_decomp_algorithm_
|
protected |
◆ max_decomp_weight_
|
protected |
◆ max_isotope_
|
protected |
◆ max_mz_
|
protected |
◆ max_number_aa_per_decomp_
|
protected |
◆ max_number_pivot_
|
protected |
◆ max_subscore_number_
|
protected |
◆ min_aa_weight_
|
protected |
◆ min_mz_
|
protected |
◆ name_to_residue_
mapping for the internal representation character to the actual residue
◆ permute_cache_
◆ residue_to_name_
mapping of the actual residue to the internal representing character
◆ subspec_to_sequences_
◆ tryptic_only_
|
protected |
◆ zhang_
|
protected |