| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
FeatureFinderMultiplexAlgorithm Class Reference

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

Inheritance diagram for FeatureFinderMultiplexAlgorithm:

## Public Member Functions

| FeatureFinderMultiplexAlgorithm ()
| default constructor More...
void | run (MSExperiment &exp, bool progress)
| main method for feature detection More...
FeatureMap & | getFeatureMap ()
| get methods More...
ConsensusMap & | getConsensusMap ()
MSExperiment & | getBlacklist ()
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 &param)
| 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...
Public Member Functions inherited from ProgressLogger
| ProgressLogger ()
| Constructor. More...
| ~ProgressLogger ()
| Destructor. More...
| ProgressLogger (const ProgressLogger &other)
| Copy constructor. More...
ProgressLogger & | operator= (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< MultiplexIsotopicPeakPattern > | generatePeakPatterns_ (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)
| 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< 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...
Protected Attributes inherited from ProgressLogger
LogType | type_
time_t | last_invoke_
ProgressLoggerImpl * | current_logger_

## Additional Inherited Members

Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. 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()

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
| ) |  |

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_peptide | peptide 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

  patterns | patterns of isotopic peaks we have been searching for
  filter_results | filter results for each of the patterns
  cluster_results | clusters 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

  patterns | patterns of isotopic peaks we have been searching for
  filter_results | filter results for each of the patterns
  cluster_results | clusters 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_min | minimum charge
  charge_max | maximum charge
  peaks_per_peptide_max | maximum number of isotopes in peptide
  mass_pattern_list | mass shifts due to labelling

Returns
  list of m/z shifts

## ◆ getBlacklist()

MSExperiment& getBlacklist | ( |  | ) |

## ◆ getConsensusMap()

ConsensusMap& getConsensusMap | ( |  | ) |

## ◆ getFeatureMap()

FeatureMap& getFeatureMap | ( |  | ) |

get methods

Referenced by UTILProteomicsLFQ::calculateSeeds_().

## ◆ run()

void run | ( | MSExperiment & | exp,
|  | bool | progress
| ) |  |

main method for feature detection

Referenced by UTILProteomicsLFQ::calculateSeeds_().

## 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