Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
Classes | Public Types | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
CompNovoIdentificationBase Class Referenceabstract

run with CompNovoIdentificationBase More...

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

Inheritance diagram for CompNovoIdentificationBase:
DefaultParamHandler CompNovoIdentification CompNovoIdentificationCID

Classes

class  Permut
 Simple class to store permutations and a score. More...
 

Public Types

typedef
CompNovoIonScoringBase::IonScore 
IonScore
 

Public Member Functions

CompNovoIdentificationBaseoperator= (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 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 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, DoubleRealaa_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< 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 CompNovoIdentificationBase

Member Typedef Documentation

Constructor & Destructor Documentation

default constructor

copy constructor

virtual ~CompNovoIdentificationBase ( )
virtual

destructor

Member Function Documentation

DoubleReal compareSpectra_ ( const PeakSpectrum s1,
const PeakSpectrum s2 
)
protected

compares two spectra

Size countMissedCleavagesTryptic_ ( const String peptide) const
protected
DoubleReal estimatePrecursorWeight_ ( const PeakSpectrum ETD_spec,
Size charge 
)
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

void filterDecomps_ ( std::vector< MassDecomposition > &  decomps)
protected

filters the decomps by the amino acid frequencies

void filterPermuts_ ( std::set< String > &  permut)
protected

filters the permutations

void getCIDSpectrum_ ( PeakSpectrum spec,
const String sequence,
Size  charge,
DoubleReal  prefix = 0.0,
DoubleReal  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

void getCIDSpectrumLight_ ( PeakSpectrum spec,
const String sequence,
DoubleReal  prefix,
DoubleReal  suffix 
)
protected

fills the spec with b and y ions, no other ion types or doubly charged variants are used

void getDecompositions_ ( std::vector< MassDecomposition > &  decomps,
DoubleReal  mass,
bool  no_caching = false 
)
protected

produces mass decompositions using the given mass

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

performs an ProteinIdentification run on a PeakMap

Implemented in CompNovoIdentification, and CompNovoIdentificationCID.

AASequence getModifiedAASequence_ ( const String sequence)
protected

returns a modified AASequence from a given internal representation

String getModifiedStringFromAASequence_ ( const AASequence sequence)
protected

returns the internal representation of a given AASequence

void initIsotopeDistributions_ ( )
protected

initializes the score distribution precalculated for the use in spectrum generation

assignment operator

void permute_ ( String  prefix,
String  s,
std::set< String > &  permutations 
)
protected

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

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 
)
protected

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

void updateMembers_ ( )
protectedvirtual

update members method from DefaultParamHandler to update the members

Reimplemented from DefaultParamHandler.

Reimplemented in CompNovoIdentificationCID.

void windowMower_ ( PeakSpectrum spec,
DoubleReal  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

Map<char, DoubleReal> aa_to_weight_
protected

masses of the amino acids

Map<DoubleReal, std::vector<MassDecomposition> > decomp_cache_
protected
DoubleReal decomp_weights_precision_
protected
DoubleReal fragment_mass_tolerance_
protected
Map<Size, std::vector<DoubleReal> > isotope_distributions_
protected
MassDecompositionAlgorithm mass_decomp_algorithm_
protected
DoubleReal max_decomp_weight_
protected
Size max_isotope_
protected
DoubleReal max_mz_
protected
Size max_number_aa_per_decomp_
protected
Size max_number_pivot_
protected
Size max_subscore_number_
protected
DoubleReal min_aa_weight_
protected
DoubleReal min_mz_
protected
Map<char, const Residue *> name_to_residue_
protected

mapping for the internal representation character to the actual residue

Map<String, std::set<String> > permute_cache_
protected
Map<const Residue *, char> residue_to_name_
protected

mapping of the actual residue to the internal representing character

Map<Size, Map<Size, std::set<String> > > subspec_to_sequences_
protected
bool tryptic_only_
protected
ZhangSimilarityScore zhang_
protected

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:25 using doxygen 1.8.5