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OfflinePrecursorIonSelection Class Reference

Implements different algorithms for precursor ion selection. More...

#include <OpenMS/ANALYSIS/TARGETED/OfflinePrecursorIonSelection.h>

Inheritance diagram for OfflinePrecursorIonSelection:
DefaultParamHandler

Public Types

typedef PSLPFormulation::IndexTriple IndexTriple
 

Public Member Functions

 OfflinePrecursorIonSelection ()
 
virtual ~OfflinePrecursorIonSelection ()
 
template<typename InputPeakType >
void makePrecursorSelectionForKnownLCMSMap (const FeatureMap &features, const MSExperiment< InputPeakType > &experiment, MSExperiment< InputPeakType > &ms2, std::set< Int > &charges_set, bool feature_based)
 Makes the precursor selection for a given feature map, either feature or scan based. More...
 
template<typename InputPeakType >
void getMassRanges (const FeatureMap &features, const MSExperiment< InputPeakType > &experiment, std::vector< std::vector< std::pair< Size, Size > > > &indices)
 Calculates the mass ranges for each feature and stores them as indices of the raw data. More...
 
void createProteinSequenceBasedLPInclusionList (String include, String rt_model_file, String pt_model_file, FeatureMap &precursors)
 
void setLPSolver (LPWrapper::SOLVER solver)
 
LPWrapper::SOLVER getLPSolver ()
 
- 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...
 

Private Member Functions

template<typename InputPeakType >
void calculateXICs_ (const FeatureMap &features, const std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const MSExperiment< InputPeakType > &experiment, const std::set< Int > &charges_set, std::vector< std::vector< std::pair< Size, double > > > &xics)
 Calculate the sum of intensities of relevant features for each scan separately. More...
 
template<typename InputPeakType >
void checkMassRanges_ (std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const MSExperiment< InputPeakType > &experiment)
 Eliminates overlapping peaks. More...
 
template<typename T >
void updateExclusionList_ (std::vector< std::pair< T, Size > > &exclusion_list)
 
void updateExclusionList_ (std::map< std::pair< double, double >, Size, PairComparatorSecondElement< std::pair< double, double > > > &exclusion_list)
 

Private Attributes

LPWrapper::SOLVER solver_
 

Additional Inherited Members

- Protected Member Functions inherited from DefaultParamHandler
virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. 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< 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

Implements different algorithms for precursor ion selection.

Implements different algorithms for precursor ion selection, either based on a whole FeatureMap (e.g. like with LC-MALDI MS data) or based on single scans (e.g. with LC-ESI MS data).

Member Typedef Documentation

Constructor & Destructor Documentation

virtual ~OfflinePrecursorIonSelection ( )
virtual

Member Function Documentation

void calculateXICs_ ( const FeatureMap features,
const std::vector< std::vector< std::pair< Size, Size > > > &  mass_ranges,
const MSExperiment< InputPeakType > &  experiment,
const std::set< Int > &  charges_set,
std::vector< std::vector< std::pair< Size, double > > > &  xics 
)
private

Calculate the sum of intensities of relevant features for each scan separately.

References MSExperiment< PeakT, ChromatogramPeakT >::size().

void checkMassRanges_ ( std::vector< std::vector< std::pair< Size, Size > > > &  mass_ranges,
const MSExperiment< InputPeakType > &  experiment 
)
private

Eliminates overlapping peaks.

void createProteinSequenceBasedLPInclusionList ( String  include,
String  rt_model_file,
String  pt_model_file,
FeatureMap precursors 
)
LPWrapper::SOLVER getLPSolver ( )
inline
void getMassRanges ( const FeatureMap features,
const MSExperiment< InputPeakType > &  experiment,
std::vector< std::vector< std::pair< Size, Size > > > &  indices 
)

Calculates the mass ranges for each feature and stores them as indices of the raw data.

Parameters
featuresInput feature map
experimentInput raw data
indicesThe boundaries of the features as indices in the raw data

References MSExperiment< PeakT, ChromatogramPeakT >::begin(), MSExperiment< PeakT, ChromatogramPeakT >::empty(), MSExperiment< PeakT, ChromatogramPeakT >::end(), MSExperiment< PeakT, ChromatogramPeakT >::RTBegin(), and MSExperiment< PeakT, ChromatogramPeakT >::size().

void makePrecursorSelectionForKnownLCMSMap ( const FeatureMap features,
const MSExperiment< InputPeakType > &  experiment,
MSExperiment< InputPeakType > &  ms2,
std::set< Int > &  charges_set,
bool  feature_based 
)
void setLPSolver ( LPWrapper::SOLVER  solver)
inline
void updateExclusionList_ ( std::vector< std::pair< T, Size > > &  exclusion_list)
private
void updateExclusionList_ ( std::map< std::pair< double, double >, Size, PairComparatorSecondElement< std::pair< double, double > > > &  exclusion_list)
inlineprivate

Member Data Documentation

LPWrapper::SOLVER solver_
private

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11