OpenMS
FeatureFinderMultiplexAlgorithm Class Reference

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderMultiplexAlgorithm.h>

Inheritance diagram for FeatureFinderMultiplexAlgorithm:
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Collaboration diagram for FeatureFinderMultiplexAlgorithm:
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Public Member Functions

 FeatureFinderMultiplexAlgorithm ()
 default constructor More...
 
void run (MSExperiment &exp, bool progress)
 main method for feature detection More...
 
FeatureMapgetFeatureMap ()
 get methods More...
 
ConsensusMapgetConsensusMap ()
 
MSExperimentgetBlacklist ()
 
- 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...
 
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...
 
- Public Member Functions inherited from ProgressLogger
 ProgressLogger ()
 Constructor. More...
 
virtual ~ProgressLogger ()
 Destructor. More...
 
 ProgressLogger (const ProgressLogger &other)
 Copy constructor. More...
 
ProgressLoggeroperator= (const ProgressLogger &other)
 Assignment Operator. More...
 
void setLogType (LogType type) const
 Sets the progress log that should be used. The default type is NONE! More...
 
LogType getLogType () const
 Returns the type of progress log being used. More...
 
void startProgress (SignedSize begin, SignedSize end, const String &label) const
 Initializes the progress display. More...
 
void setProgress (SignedSize value) const
 Sets the current progress. More...
 
void endProgress () const
 Ends the progress display. More...
 
void nextProgress () const
 increment progress by 1 (according to range begin-end) More...
 

Protected Member Functions

std::vector< MultiplexIsotopicPeakPatterngeneratePeakPatterns_ (int charge_min, int charge_max, int peaks_per_peptide_max, const std::vector< MultiplexDeltaMasses > &mass_pattern_list)
 generate list of m/z shifts More...
 
void correctPeptideIntensities_ (const MultiplexIsotopicPeakPattern &pattern, std::map< size_t, SplinePackage > &spline_chromatograms, const std::vector< double > &rt_peptide, std::vector< double > &intensity_peptide) const
 determine ratios through linear regression and correct peptide intensities More...
 
std::vector< double > determinePeptideIntensitiesCentroided_ (const MultiplexIsotopicPeakPattern &pattern, const std::multimap< size_t, MultiplexSatelliteCentroided > &satellites)
 calculate peptide intensities More...
 
std::vector< double > determinePeptideIntensitiesProfile_ (const MultiplexIsotopicPeakPattern &pattern, const std::multimap< size_t, MultiplexSatelliteProfile > &satellites)
 calculate peptide intensities More...
 
void generateMapsCentroided_ (const std::vector< MultiplexIsotopicPeakPattern > &patterns, const std::vector< MultiplexFilteredMSExperiment > &filter_results, std::vector< std::map< int, GridBasedCluster > > &cluster_results)
 generates consensus and feature maps containing all peptide multiplets More...
 
void generateMapsProfile_ (const std::vector< MultiplexIsotopicPeakPattern > &patterns, const std::vector< MultiplexFilteredMSExperiment > &filter_results, const std::vector< std::map< int, GridBasedCluster > > &cluster_results)
 generates consensus and feature maps containing all peptide multiplets More...
 
- 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

MSExperiment exp_profile_
 
MSExperiment exp_centroid_
 
bool centroided_
 
ProgressLogger prog_log_
 
bool progress_
 
unsigned charge_min_
 
unsigned charge_max_
 
unsigned isotopes_per_peptide_min_
 
unsigned isotopes_per_peptide_max_
 
std::map< String, double > label_mass_shift_
 
FeatureMap feature_map_
 
ConsensusMap consensus_map_
 
MSExperiment exp_blacklist_
 
- 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...
 
- Protected Attributes inherited from ProgressLogger
LogType type_
 
time_t last_invoke_
 
ProgressLoggerImplcurrent_logger_
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD , GUI , NONE }
 Possible log types. More...
 
- 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...
 
- Static Protected Member Functions inherited from ProgressLogger
static String logTypeToFactoryName_ (LogType type)
 Return the name of the factory product used for this log type. More...
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Constructor & Destructor Documentation

◆ FeatureFinderMultiplexAlgorithm()

default constructor

Member Function Documentation

◆ correctPeptideIntensities_()

void correctPeptideIntensities_ ( const MultiplexIsotopicPeakPattern pattern,
std::map< size_t, SplinePackage > &  spline_chromatograms,
const std::vector< double > &  rt_peptide,
std::vector< double > &  intensity_peptide 
) const
protected

determine ratios through linear regression and correct peptide intensities

In most labelled mass spectrometry experiments, the fold change i.e. ratio and not the individual peptide intensities are of primary interest. For that reason, we determine the ratios from interpolated chromatogram data points directly, and then correct the current ones.

Parameters
intensity_peptidepeptide intensities to be corrected

◆ determinePeptideIntensitiesCentroided_()

std::vector<double> determinePeptideIntensitiesCentroided_ ( const MultiplexIsotopicPeakPattern pattern,
const std::multimap< size_t, MultiplexSatelliteCentroided > &  satellites 
)
protected

calculate peptide intensities

Parameters
pattern
satellites
Returns
vector with intensities for each of the peptides

◆ determinePeptideIntensitiesProfile_()

std::vector<double> determinePeptideIntensitiesProfile_ ( const MultiplexIsotopicPeakPattern pattern,
const std::multimap< size_t, MultiplexSatelliteProfile > &  satellites 
)
protected

calculate peptide intensities

Parameters
pattern
satellites
Returns
vector with intensities for each of the peptides

◆ generateMapsCentroided_()

void generateMapsCentroided_ ( const std::vector< MultiplexIsotopicPeakPattern > &  patterns,
const std::vector< MultiplexFilteredMSExperiment > &  filter_results,
std::vector< std::map< int, GridBasedCluster > > &  cluster_results 
)
protected

generates consensus and feature maps containing all peptide multiplets

Parameters
patternspatterns of isotopic peaks we have been searching for
filter_resultsfilter results for each of the patterns
cluster_resultsclusters of filter results

◆ generateMapsProfile_()

void generateMapsProfile_ ( const std::vector< MultiplexIsotopicPeakPattern > &  patterns,
const std::vector< MultiplexFilteredMSExperiment > &  filter_results,
const std::vector< std::map< int, GridBasedCluster > > &  cluster_results 
)
protected

generates consensus and feature maps containing all peptide multiplets

Parameters
patternspatterns of isotopic peaks we have been searching for
filter_resultsfilter results for each of the patterns
cluster_resultsclusters of filter results

◆ generatePeakPatterns_()

std::vector<MultiplexIsotopicPeakPattern> generatePeakPatterns_ ( int  charge_min,
int  charge_max,
int  peaks_per_peptide_max,
const std::vector< MultiplexDeltaMasses > &  mass_pattern_list 
)
protected

generate list of m/z shifts

Parameters
charge_minminimum charge
charge_maxmaximum charge
peaks_per_peptide_maxmaximum number of isotopes in peptide
mass_pattern_listmass shifts due to labelling
Returns
list of m/z shifts

◆ getBlacklist()

MSExperiment& getBlacklist ( )

◆ getConsensusMap()

ConsensusMap& getConsensusMap ( )

◆ getFeatureMap()

FeatureMap& getFeatureMap ( )

get methods

◆ run()

void run ( MSExperiment exp,
bool  progress 
)

main method for feature detection

Member Data Documentation

◆ centroided_

bool centroided_
protected

◆ charge_max_

unsigned charge_max_
protected

◆ charge_min_

unsigned charge_min_
protected

◆ consensus_map_

ConsensusMap consensus_map_
protected

◆ exp_blacklist_

MSExperiment exp_blacklist_
protected

◆ exp_centroid_

MSExperiment exp_centroid_
protected

◆ exp_profile_

MSExperiment exp_profile_
protected

◆ feature_map_

FeatureMap feature_map_
protected

◆ isotopes_per_peptide_max_

unsigned isotopes_per_peptide_max_
protected

◆ isotopes_per_peptide_min_

unsigned isotopes_per_peptide_min_
protected

◆ label_mass_shift_

std::map<String, double> label_mass_shift_
protected

◆ prog_log_

ProgressLogger prog_log_
protected

◆ progress_

bool progress_
protected