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).
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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.
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 | ||
) |
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(), MSExperiment< PeakT, ChromatogramPeakT >::empty(), MSExperiment< PeakT, ChromatogramPeakT >::end(), MSExperiment< PeakT, ChromatogramPeakT >::RTBegin(), and MSExperiment< PeakT, ChromatogramPeakT >::size().
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(), PSLPFormulation::createAndSolveILPForKnownLCMSMapFeatureBased(), Peak1D::getMZ(), MSSpectrum< PeakT >::getRT(), DIntervalBase< D >::maxY(), DIntervalBase< D >::minY(), OPENMS_PRECONDITION, 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(), and MSSpectrum< PeakT >::sortByIntensity().
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OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 12:49:29 using doxygen 1.8.11 |