| OpenMS 2.5.0

Public Types | Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
OfflinePrecursorIonSelection Class Reference

Implements different algorithms for precursor ion selection. More...

`#include <OpenMS/ANALYSIS/TARGETED/OfflinePrecursorIonSelection.h>`

Inheritance diagram for OfflinePrecursorIonSelection:

## Public Types

typedef PSLPFormulation::IndexTriple | IndexTriple

## Public Member Functions

| OfflinePrecursorIonSelection ()
| ~OfflinePrecursorIonSelection () override
void | makePrecursorSelectionForKnownLCMSMap (const FeatureMap &features, const PeakMap &experiment, PeakMap &ms2, std::set< Int > &charges_set, bool feature_based)
| Makes the precursor selection for a given feature map, either feature or scan based. More...
void | getMassRanges (const FeatureMap &features, const PeakMap &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 &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...

## Private Types

typedef std::map< std::pair< double, double >, int, PairComparatorSecondElement< std::pair< double, double > > > | ExclusionListType_

## Private Member Functions

void | calculateXICs_ (const FeatureMap &features, const std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const PeakMap &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...
void | checkMassRanges_ (std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const PeakMap &experiment)
| Eliminates overlapping peaks. More...
void | updateExclusionList_ (ExclusionListType_ &exclusion_list) const
| reduce scan count for each entry, and remove every entry which has reached 0 counts More...

## 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...

## Detailed Description

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_mz_peak_distance | float | 2.0 | min: 1.0e-04 | The minimal distance (in Th) between two peaks for concurrent selection for fragmentation. Also used to define the m/z width of an exclusion window (distance +/- from m/z of precursor). If you set this lower than the isotopic envelope of a peptide, you might get multiple fragment spectra pointing to the same precursor.
mz_isolation_window | float | 2.0 | min: 0.0 | All peaks within a mass window (in Th) of a selected peak are also selected for fragmentation.
exclude_overlapping_peaks | string | false | true, false | If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection.
Exclusion:use_dynamic_exclusion | string | false | true, false | If true dynamic exclusion is applied.
Exclusion:exclusion_time | float | 100.0 | min: 0.0 | 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 | 960.0 | min: 0.0 | Minimal rt in seconds.
ProteinBasedInclusion:rt:max_rt | float | 3840.0 | min: 0.0 | Maximal rt in seconds.
ProteinBasedInclusion:rt:rt_step_size | float | 30.0 | min: 1.0 | 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: 0.0 max: 1.0 | Minimal protein probability for a protein to be considered identified.
ProteinBasedInclusion:thresholds:min_pt_weight | float | 0.5 | min: 0.0 max: 1.0 | Minimal pt weight of a precursor
ProteinBasedInclusion:thresholds:min_mz | float | 500.0 | min: 0.0 | Minimal mz to be considered in protein based LP formulation.
ProteinBasedInclusion:thresholds:max_mz | float | 5000.0 | min: 0.0 | 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: 0.0 max: 1.0 | If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified

Note:

- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.

## Member Typedef Documentation

## ◆ ExclusionListType_

typedef std::map<std::pair<double, double>, int, PairComparatorSecondElement<std::pair<double, double> > > ExclusionListType_

private

## ◆ IndexTriple

typedef PSLPFormulation::IndexTriple IndexTriple

## Constructor & Destructor Documentation

## ◆ OfflinePrecursorIonSelection()

OfflinePrecursorIonSelection | ( |  | ) |

## ◆ ~OfflinePrecursorIonSelection()

~OfflinePrecursorIonSelection | ( |  | ) |

override

## Member Function Documentation

## ◆ calculateXICs_()

void calculateXICs_ | ( | const FeatureMap & | features,
|  | const std::vector< std::vector< std::pair< Size, Size > > > & | mass_ranges,
|  | const PeakMap & | experiment,
|  | const std::set< Int > & | charges_set,
|  | std::vector< std::vector< std::pair< Size, double > > > & | xics
| ) |  |

private

Calculate the sum of intensities of relevant features for each scan separately.

## ◆ checkMassRanges_()

void checkMassRanges_ | ( | std::vector< std::vector< std::pair< Size, Size > > > & | mass_ranges,
|  | const PeakMap & | experiment
| ) |  |

private

Eliminates overlapping peaks.

## ◆ createProteinSequenceBasedLPInclusionList()

void createProteinSequenceBasedLPInclusionList | ( | String | include,
|  | String | rt_model_file,
|  | String | pt_model_file,
|  | FeatureMap & | precursors
| ) |  |

## ◆ getLPSolver()

LPWrapper::SOLVER getLPSolver | ( |  | ) |

inline

## ◆ getMassRanges()

void getMassRanges | ( | const FeatureMap & | features,
|  | const PeakMap & | 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.

Parameters

  features | Input feature map
  experiment | Input raw data
  indices | The boundaries of the features as indices in the raw data

## ◆ makePrecursorSelectionForKnownLCMSMap()

void makePrecursorSelectionForKnownLCMSMap | ( | const FeatureMap & | features,
|  | const PeakMap & | experiment,
|  | PeakMap & | ms2,
|  | std::set< Int > & | charges_set,
|  | bool | feature_based
| ) |  |

Makes the precursor selection for a given feature map, either feature or scan based.

Parameters

  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

## ◆ setLPSolver()

void setLPSolver | ( | LPWrapper::SOLVER | solver | ) |

inline

## ◆ updateExclusionList_()

void updateExclusionList_ | ( | ExclusionListType_ & | exclusion_list | ) | const

private

reduce scan count for each entry, and remove every entry which has reached 0 counts

## Member Data Documentation

## ◆ solver_

LPWrapper::SOLVER solver_

private