Implements different algorithms for precursor ion selection. More...
#include <OpenMS/ANALYSIS/TARGETED/OfflinePrecursorIonSelection.h>
 
  
 | 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 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... | |
| 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, DoubleReal > > > &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< DoubleReal, DoubleReal >, Size, PairComparatorSecondElement< std::pair< DoubleReal, DoubleReal > > > &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< 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... | |
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:| Name | Type | Default | Restrictions | Description | 
|---|---|---|---|---|
| ms2_spectra_per_rt_bin | int | 5 | min: 1 | Number of allowed MS/MS spectra in a retention time bin. | 
| min_peak_distance | float | 3 | min: 0 | The minimal distance (in Da) of two peaks in one spectrum so that they can be selected. | 
| selection_window | float | 2 | min: 0 | All peaks within a mass window (in Da) of a selected peak are also selected for fragmentation. | 
| exclude_overlapping_peaks | string | false | true, false | If true overlapping or nearby peaks (within min_peak_distance) are excluded for selection. | 
| Exclusion:use_dynamic_exclusion | string | false | true, false | If true dynamic exclusion is applied. | 
| Exclusion:exclusion_time | float | 100 | min: 0 | The time (in seconds) a feature is excluded. | 
| ProteinBasedInclusion:max_list_size | int | 1000 | min: 1 | The maximal number of precursors in the inclusion list. | 
| ProteinBasedInclusion:rt:min_rt | float | 960 | min: 0 | Minimal rt in seconds. | 
| ProteinBasedInclusion:rt:max_rt | float | 3840 | min: 0 | Maximal rt in seconds. | 
| ProteinBasedInclusion:rt:rt_step_size | float | 30 | min: 1 | rt step size in seconds. | 
| ProteinBasedInclusion:rt:rt_window_size | int | 100 | min: 1 | rt window size in seconds. | 
| ProteinBasedInclusion:thresholds:min_protein_id_probability | float | 0.95 | min: 0 max: 1 | Minimal protein probability for a protein to be considered identified. | 
| ProteinBasedInclusion:thresholds:min_pt_weight | float | 0.5 | min: 0 max: 1 | Minimal pt weight of a precursor | 
| ProteinBasedInclusion:thresholds:min_mz | float | 500 | min: 0 | Minimal mz to be considered in protein based LP formulation. | 
| ProteinBasedInclusion:thresholds:max_mz | float | 5000 | min: 0 | Minimal mz to be considered in protein based LP formulation. | 
| ProteinBasedInclusion:thresholds:use_peptide_rule | string | false | true, false | Use peptide rule instead of minimal protein id probability | 
| ProteinBasedInclusion:thresholds:min_peptide_ids | int | 2 | min: 1 | If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id | 
| ProteinBasedInclusion:thresholds:min_peptide_probability | float | 0.95 | min: 0 max: 1 | If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified | 
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Calculate the sum of intensities of relevant features for each scan separately.
References MSExperiment< PeakT, ChromatogramPeakT >::size().
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 | 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 | ||
| ) | 
| 
 | 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.
| features | Input feature map | 
| experiment | Input raw data | 
| indices | The boundaries of the features as indices in the raw data | 
References MSExperiment< PeakT, ChromatogramPeakT >::begin(), OfflinePrecursorIonSelection::checkMassRanges_(), MSExperiment< PeakT, ChromatogramPeakT >::empty(), MSExperiment< PeakT, ChromatogramPeakT >::end(), Param::getValue(), DefaultParamHandler::param_, MSExperiment< PeakT, ChromatogramPeakT >::RTBegin(), and MSExperiment< PeakT, ChromatogramPeakT >::size().
Referenced by OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap().
| 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.
| features | Input feature map | 
| experiment | Input raw data | 
| ms2 | Precursors are added as empty MS2 spectra to this MSExperiment | 
| charges_set | Allowed charge states | 
| feature_based | If true the selection is feature based, if false it is scan based and the highest signals in each spectrum are chosen | 
References MSExperiment< PeakT, ChromatogramPeakT >::addSpectrum(), MSExperiment< PeakT, ChromatogramPeakT >::begin(), IntList::create(), PSLPFormulation::createAndSolveILPForKnownLCMSMapFeatureBased(), OfflinePrecursorIonSelection::getMassRanges(), Peak1D::getMZ(), MSSpectrum< PeakT >::getRT(), Param::getValue(), DIntervalBase< D >::maxY(), DIntervalBase< D >::minY(), OPENMS_PRECONDITION, DefaultParamHandler::param_, MSExperiment< PeakT, ChromatogramPeakT >::RTBegin(), MSExperiment< PeakT, ChromatogramPeakT >::RTEnd(), Precursor::setCharge(), Peak1D::setIntensity(), DIntervalBase< D >::setMaxY(), MetaInfoInterface::setMetaValue(), DIntervalBase< D >::setMinY(), MSSpectrum< PeakT >::setMSLevel(), Peak1D::setMZ(), SpectrumSettings::setPrecursors(), MSSpectrum< PeakT >::setRT(), MSExperiment< PeakT, ChromatogramPeakT >::size(), MSSpectrum< PeakT >::sortByIntensity(), and OfflinePrecursorIonSelection::updateExclusionList_().
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| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |