OpenMS
|
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderMultiplexAlgorithm.h>
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... | |
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... | |
Public Member Functions inherited from ProgressLogger | |
ProgressLogger () | |
Constructor. More... | |
virtual | ~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) 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< 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 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_ |
default constructor
|
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.
intensity_peptide | peptide intensities to be corrected |
|
protected |
calculate peptide intensities
pattern | |
satellites |
|
protected |
calculate peptide intensities
pattern | |
satellites |
|
protected |
generates consensus and feature maps containing all peptide multiplets
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 |
|
protected |
generates consensus and feature maps containing all peptide multiplets
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 |
|
protected |
generate list of m/z shifts
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 |
MSExperiment& getBlacklist | ( | ) |
ConsensusMap& getConsensusMap | ( | ) |
FeatureMap& getFeatureMap | ( | ) |
get methods
void run | ( | MSExperiment & | exp, |
bool | progress | ||
) |
main method for feature detection
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |