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 () |
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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, 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 | |
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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... | |
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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 |
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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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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 | ||
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void getMassRanges | ( | const FeatureMap & | features, |
const MSExperiment< InputPeakType > & | experiment, | ||
std::vector< std::vector< std::pair< Size, Size > > > & | indices | ||
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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 | ||
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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(), 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 2.0.0 | Documentation generated on Fri May 29 2015 17:20:41 using doxygen 1.8.9.1 |