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OpenMS
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Feature trace in mass dimension for FLASHDeconv This class performs mass tracing on the deconvolved masses by FLASHDeconvAlgorithm In other words, per spectrum deconvolved masses are converted into deconvolved features Currently only works for MS1 spectra. (Top-down DIA is not yet used much). Every time an MS1 spectrum is deconvolved, the relevant information is stored in this class. Tracing is performed at the end of FLASHDeconv run. This class also comes with tsv, TopFD, ProMex format output functions. More...
#include <OpenMS/ANALYSIS/TOPDOWN/MassFeatureTrace.h>
Public Types | |
| typedef FLASHDeconvHelperStructs::PrecalculatedAveragine | PrecalculatedAveragine |
| typedef FLASHDeconvHelperStructs::LogMzPeak | LogMzPeak |
Public Member Functions | |
| MassFeatureTrace () | |
| constructor More... | |
| ~MassFeatureTrace () override=default | |
| destructor More... | |
| MassFeatureTrace (const MassFeatureTrace &)=default | |
| copy constructor More... | |
| MassFeatureTrace (MassFeatureTrace &&other)=default | |
| move constructor More... | |
| MassFeatureTrace & | operator= (const MassFeatureTrace &fd)=default |
| assignment operator More... | |
| MassFeatureTrace & | operator= (MassFeatureTrace &&fd)=default |
| void | storeInformationFromDeconvolvedSpectrum (DeconvolvedSpectrum &deconvolved_spectrum) |
| Obtain and store information from deconvolved_spectrum (necessary information for mass tracing afterwards) More... | |
| std::vector< FLASHDeconvHelperStructs::MassFeature > | findFeatures (const PrecalculatedAveragine &averagine) |
| Find mass features. 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... | |
| 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_ () override |
| This method is used to update extra member variables at the end of the setParameters() method. More... | |
| Protected Member Functions inherited from DefaultParamHandler | |
| void | defaultsToParam_ () |
| Updates the parameters after the defaults have been set in the constructor. More... | |
Private Attributes | |
| double | min_isotope_cosine_ |
| cosine thresholds for scoring and filtering More... | |
| std::map< double, std::map< double, PeakGroup > > | peak_group_map_ |
| peak group information is stored in here for tracing More... | |
Additional Inherited Members | |
| Static Public Member Functions inherited from DefaultParamHandler | |
| static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") |
| Writes all parameters to meta values. More... | |
| 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... | |
Feature trace in mass dimension for FLASHDeconv This class performs mass tracing on the deconvolved masses by FLASHDeconvAlgorithm In other words, per spectrum deconvolved masses are converted into deconvolved features Currently only works for MS1 spectra. (Top-down DIA is not yet used much). Every time an MS1 spectrum is deconvolved, the relevant information is stored in this class. Tracing is performed at the end of FLASHDeconv run. This class also comes with tsv, TopFD, ProMex format output functions.
| MassFeatureTrace | ( | ) |
constructor
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overridedefault |
destructor
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default |
copy constructor
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default |
move constructor
| std::vector<FLASHDeconvHelperStructs::MassFeature> findFeatures | ( | const PrecalculatedAveragine & | averagine | ) |
Find mass features.
| averagine | precalculated averagine for cosine calculation |
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default |
assignment operator
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default |
| void storeInformationFromDeconvolvedSpectrum | ( | DeconvolvedSpectrum & | deconvolved_spectrum | ) |
Obtain and store information from deconvolved_spectrum (necessary information for mass tracing afterwards)
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overrideprotectedvirtual |
This method is used to update extra member variables at the end of the setParameters() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from DefaultParamHandler.
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private |
cosine thresholds for scoring and filtering
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private |
peak group information is stored in here for tracing
1.9.1 
