run with CompNovoIdentificationBase More...
#include <OpenMS/ANALYSIS/DENOVO/CompNovoIdentificationBase.h>
 
  
 | 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< 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  More... | |
| void | filterDecomps_ (std::vector< MassDecomposition > &decomps) | 
| filters the decomps by the amino acid frequencies  More... | |
| void | getDecompositions_ (std::vector< MassDecomposition > &decomps, DoubleReal 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, DoubleReal prefix, DoubleReal 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, 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  More... | |
| void | initIsotopeDistributions_ () | 
| initializes the score distribution precalculated for the use in spectrum generation  More... | |
| 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  More... | |
| 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  More... | |
| DoubleReal | 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 < DoubleReal > > | isotope_distributions_ | 
| Map< char, DoubleReal > | aa_to_weight_ | 
| masses of the amino acids  More... | |
| 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_ | 
|  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... | |
run with CompNovoIdentificationBase
default constructor
| CompNovoIdentificationBase | ( | const CompNovoIdentificationBase & | source | ) | 
copy constructor
| 
 | virtual | 
destructor
| 
 | protected | 
compares two spectra
| 
 | 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
| 
 | protected | 
filters the decomps by the amino acid frequencies
| 
 | protected | 
filters the permutations
| 
 | protected | 
fills the spectrum with b,y ions, multiple charged variants; if prefix and suffix weights are given, the sequence is treated as tag
| 
 | protected | 
fills the spec with b and y ions, no other ion types or doubly charged variants are used
| 
 | protected | 
produces mass decompositions using the given mass
| 
 | pure virtual | 
performs an ProteinIdentification run on a PeakMap
Implemented in CompNovoIdentification, and CompNovoIdentificationCID.
| 
 | protected | 
returns a modified AASequence from a given internal representation
| 
 | protected | 
returns the internal representation of a given AASequence
| 
 | protected | 
initializes the score distribution precalculated for the use in spectrum generation
| CompNovoIdentificationBase& operator= | ( | const CompNovoIdentificationBase & | source | ) | 
assignment operator
permuts the String s adds the prefix and stores the results in permutations
| 
 | protected | 
selects pivot ion of the given range using the scores given in CID_nodes
| 
 | protectedvirtual | 
update members method from DefaultParamHandler to update the members
Reimplemented from DefaultParamHandler.
Reimplemented in CompNovoIdentificationCID.
| 
 | protected | 
keep for each window of size windowsize in the m/z range of the spectrum exactly no_peaks
| 
 | protected | 
masses of the amino acids
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
mapping for the internal representation character to the actual residue
mapping of the actual residue to the internal representing character
| 
 | protected | 
| 
 | protected | 
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:25 using doxygen 1.8.5 |