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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).

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
ms2_spectra_per_rt_bin int5 min: 1Number of allowed MS/MS spectra in a retention time bin.
min_peak_distance float3 min: 0The minimal distance (in Da) of two peaks in one spectrum so that they can be selected.
selection_window float2 min: 0All peaks within a mass window (in Da) of a selected peak are also selected for fragmentation.
exclude_overlapping_peaks stringfalse true, falseIf true overlapping or nearby peaks (within min_peak_distance) are excluded for selection.
Exclusion:use_dynamic_exclusion stringfalse true, falseIf true dynamic exclusion is applied.
Exclusion:exclusion_time float100 min: 0The time (in seconds) a feature is excluded.
ProteinBasedInclusion:max_list_size int1000 min: 1The maximal number of precursors in the inclusion list.
ProteinBasedInclusion:rt:min_rt float960 min: 0Minimal rt in seconds.
ProteinBasedInclusion:rt:max_rt float3840 min: 0Maximal rt in seconds.
ProteinBasedInclusion:rt:rt_step_size float30 min: 1rt step size in seconds.
ProteinBasedInclusion:rt:rt_window_size int100 min: 1rt window size in seconds.
ProteinBasedInclusion:thresholds:min_protein_id_probability float0.95 min: 0 max: 1Minimal protein probability for a protein to be considered identified.
ProteinBasedInclusion:thresholds:min_pt_weight float0.5 min: 0 max: 1Minimal pt weight of a precursor
ProteinBasedInclusion:thresholds:min_mz float500 min: 0Minimal mz to be considered in protein based LP formulation.
ProteinBasedInclusion:thresholds:max_mz float5000 min: 0Minimal mz to be considered in protein based LP formulation.
ProteinBasedInclusion:thresholds:use_peptide_rule stringfalse true, falseUse peptide rule instead of minimal protein id probability
ProteinBasedInclusion:thresholds:min_peptide_ids int2 min: 1If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id
ProteinBasedInclusion:thresholds:min_peptide_probability float0.95 min: 0 max: 1If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified

Note:

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.

References Param::getValue(), and DefaultParamHandler::param_.

Referenced by OfflinePrecursorIonSelection::getMassRanges().

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 
)
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 Wed Mar 30 2016 16:18:44 using doxygen 1.8.5