| OpenMS 2.5.0

Classes | Public Types | Public Member Functions | Protected Member Functions | Static Protected Member Functions | Protected Attributes | Private Attributes | List of all members
CompNovoIdentificationBase Class Referenceabstract
Analysis » Identification

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...
| ~CompNovoIdentificationBase () override
| 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 &param)
| 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_ () override
| 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...
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)
| 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...

## Static Protected Member Functions

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...

## 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< 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...

## Private Attributes

Map< Size, std::vector< double > > | isotope_distributions_

## Detailed Description

run with CompNovoIdentificationBase

## Member Typedef Documentation

## ◆ IonScore

typedef CompNovoIonScoringBase::IonScore IonScore

## Constructor & Destructor Documentation

## ◆ CompNovoIdentificationBase() [1/2]

CompNovoIdentificationBase | ( |  | ) |

default constructor

## ◆ CompNovoIdentificationBase() [2/2]

CompNovoIdentificationBase | ( | const CompNovoIdentificationBase & | source | ) |

copy constructor

## ◆ ~CompNovoIdentificationBase()

~CompNovoIdentificationBase | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ compareSpectra_()

double compareSpectra_ | ( | const PeakSpectrum & | s1,
|  | const PeakSpectrum & | s2
| ) |  |

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 | ) |

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 CompNovoIdentification, and CompNovoIdentificationCID.

## ◆ 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=()

CompNovoIdentificationBase& operator= | ( | const CompNovoIdentificationBase & | source | ) |

assignment operator

## ◆ permute_()

static void permute_ | ( | const String & | prefix,
|  | String | s,
|  | std::set< String > & | permutations
| ) |  |

static protected

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

## ◆ selectPivotIons_()

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`
| ) |  |

protected

selects pivot ion of the given range using the scores given in CID_nodes

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

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_

Map<char, double> aa_to_weight_

protected

masses of the amino acids

## ◆ decomp_cache_

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_

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_

Map<char, const Residue *> name_to_residue_

protected

mapping for the internal representation character to the actual residue

## ◆ permute_cache_

Map<String, std::set<String> > permute_cache_

protected

## ◆ residue_to_name_

Map<const Residue *, char> residue_to_name_

protected

mapping of the actual residue to the internal representing character

## ◆ subspec_to_sequences_

Map<Size, Map<Size, std::set<String> > > subspec_to_sequences_

protected

## ◆ tryptic_only_

bool tryptic_only_

protected

## ◆ zhang_

ZhangSimilarityScore zhang_

protected