| OpenMS 2.5.0

Classes | Public Types | Protected Member Functions | Static Protected Member Functions | List of all members
SpectraMerger Class Reference

Merges blocks of MS or MS2 spectra. More...

`#include <OpenMS/FILTERING/TRANSFORMERS/SpectraMerger.h>`

Inheritance diagram for SpectraMerger:

## Classes

class | SpectraDistance_

## Public Types

typedef Map< Size, std::vector< Size > > | MergeBlocks
| blocks of spectra (master-spectrum index to sacrifice-spectra(the ones being merged into the master-spectrum)) More...
typedef Map< Size, std::vector< std::pair< Size, double > > > | AverageBlocks
| blocks of spectra (master-spectrum index to update to spectra to average over) More...
Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. More...

## Public Member Functions

| SpectraMerger ()
| default constructor More...
| SpectraMerger (const SpectraMerger &source)
| copy constructor More...
| ~SpectraMerger () override
| destructor More...
SpectraMerger & | operator= (const SpectraMerger &source)
| assignment operator More...
template<typename MapType >
void | mergeSpectraBlockWise (MapType &exp)
template<typename MapType >
void | mergeSpectraPrecursors (MapType &exp)
| merges spectra with similar precursors (must have MS2 level) More...
template<typename MapType >
void | average (MapType &exp, const String &average_type)
| average over neighbouring spectra More...
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...
Public Member Functions inherited from ProgressLogger
| ProgressLogger ()
| Constructor. More...
| ~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

template<typename MapType >
void | mergeSpectra_ (MapType &exp, const MergeBlocks &spectra_to_merge, const UInt ms_level)
| merges blocks of spectra of a certain level More...
template<typename MapType >
void | averageProfileSpectra_ (MapType &exp, const AverageBlocks &spectra_to_average_over, const UInt ms_level)
| average spectra (profile mode) More...
template<typename MapType >
void | averageCentroidSpectra_ (MapType &exp, const AverageBlocks &spectra_to_average_over, const UInt ms_level)
| average spectra (centroid mode) 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...

## Static Protected Member Functions

static bool | compareByFirst (std::pair< double, double > i, std::pair< double, double > j)
| comparator for sorting peaks (m/z, intensity) 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...

## Additional Inherited Members

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_
Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_

## Detailed Description

Merges blocks of MS or MS2 spectra.

Parameter's are accessible via the DefaultParamHandler.

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
mz_binning_width | float | 5.0 | min: 0.0 | minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct. Closer data points or peaks will be merged.
mz_binning_width_unit | string | ppm | Da, ppm | Unit in which the distance between two data points or peaks is given.
sort_blocks | string | RT_ascending | RT_ascending, RT_descending | Sort blocks by before merging them (useful for precursor order)
average_gaussian:spectrum_type | string | automatic | profile, centroid, automatic | Spectrum type of the MS level to be averaged
average_gaussian:ms_level | int | 1 | min: 1 | Average spectra of this level. All other spectra remain unchanged.
average_gaussian:rt_FWHM | float | 5.0 | min: 0.0 max: 1.0e11 | FWHM of Gauss curve in seconds to be averaged over.
average_gaussian:cutoff | float | 0.01 | min: 0.0 max: 1.0 | Intensity cutoff for Gaussian. The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average.
average_tophat:spectrum_type | string | automatic | profile, centroid, automatic | Spectrum type of the MS level to be averaged
average_tophat:ms_level | int | 1 | min: 1 | Average spectra of this level. All other spectra remain unchanged.
average_tophat:rt_range | float | 5.0 | min: 0.0 max: 1.0e11 | RT range to be averaged over, i.e. +/-(RT range)/2 from each spectrum.
average_tophat:rt_unit | string | scans | scans, seconds | Unit for RT range.
block_method:ms_levels | int list | [1] | min: 1 | Merge spectra of this level. All spectra with other MS levels remain untouched.
block_method:rt_block_size | int | 5 | min: 1 | Maximum number of scans to be summed up.
block_method:rt_max_length | float | 0.0 | min: 0.0 max: 1.0e11 | Maximum RT size of the block in seconds (0.0 = no size restriction).
precursor_method:mz_tolerance | float | 1.0e-04 | min: 0.0 | Max m/z distance of the precursor entries of two spectra to be merged in [Da].
precursor_method:rt_tolerance | float | 5.0 | min: 0.0 | Max RT distance of the precursor entries of two spectra to be merged in [s].

Note:

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

## Member Typedef Documentation

## ◆ AverageBlocks

typedef Map<Size, std::vector<std::pair<Size, double> > > AverageBlocks

blocks of spectra (master-spectrum index to update to spectra to average over)

## ◆ MergeBlocks

typedef Map<Size, std::vector<Size> > MergeBlocks

blocks of spectra (master-spectrum index to sacrifice-spectra(the ones being merged into the master-spectrum))

## Constructor & Destructor Documentation

## ◆ SpectraMerger() [1/2]

SpectraMerger | ( |  | ) |

default constructor

## ◆ SpectraMerger() [2/2]

SpectraMerger | ( | const SpectraMerger & | source | ) |

copy constructor

## ◆ ~SpectraMerger()

~SpectraMerger | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ average()

void average | ( | MapType & | exp,
|  | const String & | average_type
| ) |  |

inline

average over neighbouring spectra

Parameters

  exp | experimental data to be averaged
  average_type | averaging type to be used ("gaussian" or "tophat")

References MSExperiment::begin(), SpectrumSettings::CENTROID, MSExperiment::end(), SpectrumSettings::PROFILE, MSExperiment::sortSpectra(), and OpenMS::Math::sum().

## ◆ averageCentroidSpectra_()

void averageCentroidSpectra_ | ( | MapType & | exp,
|  | const AverageBlocks & | spectra_to_average_over,
|  | const UInt | ms_level
| ) |  |

inline protected

average spectra (centroid mode)

Averages spectra in centroid mode of one MS level in an experiment. The blocks of spectra to be combined and their relative weights have previously determined. The averaged spectra are generated in two steps: (1) The m/z of all spectra in a block are collected and sorted. Their corresponding intensities are weighted. (2) m/z positions closer than mz_binning_width are combined to a single peak. The m/z are averaged and the corresponding intensities summed.

Parameters

  exp | experimental data to be averaged
  spectra_to_average_over | mapping of spectral index to set of spectra to average over with corresponding weights
  ms_level | MS level of spectra to be averaged

References MSExperiment::addSpectrum(), MSExperiment::begin(), MSSpectrum::clear(), SpectraMerger::compareByFirst(), MSExperiment::end(), ProgressLogger::endProgress(), Peak1D::setIntensity(), Peak1D::setMZ(), ProgressLogger::setProgress(), and ProgressLogger::startProgress().

## ◆ averageProfileSpectra_()

void averageProfileSpectra_ | ( | MapType & | exp,
|  | const AverageBlocks & | spectra_to_average_over,
|  | const UInt | ms_level
| ) |  |

inline protected

average spectra (profile mode)

Averages spectra in profile mode of one MS level in an experiment. The blocks of spectra to be combined and their relative weights have previously been determined. The averaged spectra are generated in two steps: (1) The m/z of all spectra in a block are collected and sorted. m/z positions closer than mz_binning_width are removed. (2) At these positions the weighted sum of all spline interpolations is calculated.

The first step ensures roughly the same sampling rate as the one of the original spectra. The exact m/z position is not crucial, since not the original intensities but the spline-interpolated intensities are used.

Parameters

  exp | experimental data to be averaged
  spectra_to_average_over | mapping of spectral index to set of spectra to average over with corresponding weights
  ms_level | MS level of spectra to be averaged

References MSExperiment::addSpectrum(), MSExperiment::begin(), MSSpectrum::clear(), MSExperiment::end(), SplineInterpolatedPeaks::Navigator::eval(), SplineInterpolatedPeaks::getNavigator(), SplineInterpolatedPeaks::getPosMax(), SplineInterpolatedPeaks::getPosMin(), Peak1D::setIntensity(), and Peak1D::setMZ().

## ◆ compareByFirst()

static bool compareByFirst | ( | std::pair< double, double > | i,
|  | std::pair< double, double > | j
| ) |  |

inline static protected

comparator for sorting peaks (m/z, intensity)

Referenced by SpectraMerger::averageCentroidSpectra_().

## ◆ mergeSpectra_()

void mergeSpectra_ | ( | MapType & | exp,
|  | const MergeBlocks & | spectra_to_merge,
|  | const UInt | ms_level
| ) |  |

inline protected

merges blocks of spectra of a certain level

Merges spectra belonging to the same block, setting their MS level to `ms_level`. All old spectra of level `ms_level` are removed, and the new consensus spectra (one per block) are added. All spectra with other MS levels remain untouched. The resulting map is NOT sorted!

References MSExperiment::addSpectrum(), MSExperiment::begin(), MSExperiment::clear(), MSExperiment::end(), SpectrumSettings::getPrecursors(), MSSpectrum::getRT(), MSExperiment::getSpectra(), SpectrumAlignment::getSpectrumAlignment(), OPENMS_LOG_INFO, OPENMS_LOG_WARN, MSSpectrum::setMSLevel(), DefaultParamHandler::setParameters(), SpectrumSettings::setPrecursors(), MSSpectrum::setRT(), Param::setValue(), MSExperiment::size(), MSSpectrum::sortByPosition(), and SpectrumSettings::unify().

## ◆ mergeSpectraBlockWise()

void mergeSpectraBlockWise | ( | MapType & | exp | ) |

inline

References MSExperiment::begin(), MSExperiment::end(), and MSExperiment::sortSpectra().

## ◆ mergeSpectraPrecursors()

void mergeSpectraPrecursors | ( | MapType & | exp | ) |

inline

merges spectra with similar precursors (must have MS2 level)

References ClusterHierarchical::cluster(), ClusterAnalyzer::cut(), OPENMS_LOG_WARN, Peak2D::setMZ(), DefaultParamHandler::setParameters(), Peak2D::setRT(), MSExperiment::size(), and MSExperiment::sortSpectra().

## ◆ operator=()

SpectraMerger& operator= | ( | const SpectraMerger & | source | ) |

assignment operator