OpenMS
2.4.0
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Annotates spectra from identifications and theoretical spectra or identifications from spectra and theoretical spectra matching with various options. More...
#include <OpenMS/CHEMISTRY/SpectrumAnnotator.h>
Public Member Functions | |
SpectrumAnnotator & | operator= (const SpectrumAnnotator &tsg) |
assignment operator More... | |
Constructors and Destructors | |
SpectrumAnnotator () | |
default constructor More... | |
SpectrumAnnotator (const SpectrumAnnotator &source) | |
copy constructor More... | |
~SpectrumAnnotator () override | |
destructor More... | |
Available annotators | |
void | annotateMatches (PeakSpectrum &spec, const PeptideHit &ph, const TheoreticalSpectrumGenerator &tg, const SpectrumAlignment &sa) const |
Adds ion match annotation to the spec input spectrum. More... | |
void | addIonMatchStatistics (PeptideIdentification &pi, MSSpectrum &spec, const TheoreticalSpectrumGenerator &tg, const SpectrumAlignment &sa) const |
Adds ion match statistics to pi PeptideIdentifcation. More... | |
void | updateMembers_ () override |
overwrite 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 Attributes | |
bool | basic_statistics_ |
bool | list_of_ions_matched_ |
bool | max_series_ |
bool | SN_statistics_ |
bool | precursor_statistics_ |
unsigned | topNmatch_fragmenterrors_ |
bool | fragmenterror_statistics_ |
bool | terminal_series_match_ratio_ |
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... | |
Static Protected Attributes | |
static const boost::regex | nt_regex_ |
static const boost::regex | ct_regex_ |
static const boost::regex | noloss_regex_ |
static const boost::regex | seriesposition_regex_ |
Additional Inherited Members | |
Protected Member Functions inherited from DefaultParamHandler | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Annotates spectra from identifications and theoretical spectra or identifications from spectra and theoretical spectra matching with various options.
default constructor
SpectrumAnnotator | ( | const SpectrumAnnotator & | source | ) |
copy constructor
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override |
destructor
void addIonMatchStatistics | ( | PeptideIdentification & | pi, |
MSSpectrum & | spec, | ||
const TheoreticalSpectrumGenerator & | tg, | ||
const SpectrumAlignment & | sa | ||
) | const |
Adds ion match statistics to pi
PeptideIdentifcation.
pi | A spectrums identifications to be annotated, looking up matches from a spectrum and the theoretical spectrum inferred from the identifications sequence |
spec | A PeakSpectrum containing the peaks from which the pi identifications are made |
tg | A TheoreticalSpectrumGenerator to infer the theoretical spectrum. Its own parameters define which ion types are referred |
sa | A SpectrumAlignment to match the theoretical spectrum with the measured. Its own parameters define the match tolerance |
The ion match statistics are added as UserParams to either the PeptideIdentification (parameters of the matching) and PeptideHit. The parameters of the TheoreticalSpectrumGenerator define the comprehensiveness of the available matching. The parameters of SpectrumAlignment define the matching tolerance. See the parameter section of this class for the available statistics.
void annotateMatches | ( | PeakSpectrum & | spec, |
const PeptideHit & | ph, | ||
const TheoreticalSpectrumGenerator & | tg, | ||
const SpectrumAlignment & | sa | ||
) | const |
Adds ion match annotation to the spec
input spectrum.
spec | A PeakSpectrum containing the peaks from which the pi identifications are made |
ph | A spectrums identifications to be used for the annotation, looking up matches from a spectrum and the theoretical spectrum inferred from the identifications sequence |
tg | A TheoreticalSpectrumGenerator to infer the theoretical spectrum. Its own parameters define which ion types are referred |
sa | A SpectrumAlignment to match the theoretical spectrum with the measured. Its own parameters define the match tolerance |
The matches are added as DataArrays to the spectrum (Names: IonName and IonMatchError). The parameters of the TheoreticalSpectrumGenerator define the comprehensiveness of the available matching. The parameters of SpectrumAlignment define the matching tolerance. See the parameter section of this class for the available options.
SpectrumAnnotator& operator= | ( | const SpectrumAnnotator & | tsg | ) |
assignment operator
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overwrite
Reimplemented from DefaultParamHandler.
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