Merges blocks of MS or MS2 spectra. More...
#include <OpenMS/FILTERING/TRANSFORMERS/SpectraMerger.h>
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)) | |
Public Member Functions | |
| SpectraMerger () | |
| default constructor | |
| SpectraMerger (const SpectraMerger &source) | |
| copy constructor | |
| virtual | ~SpectraMerger () |
| destructor | |
| SpectraMerger & | operator= (const SpectraMerger &source) |
| assignment operator | |
| template<typename MapType > | |
| void | mergeSpectraBlockWise (MapType &exp) |
| template<typename MapType > | |
| void | mergeSpectraPrecursors (MapType &exp) |
| merges spectra with similar precursors (must have MS2 level) | |
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 | |
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 | 0.0001 | min: 0 | Max m/z distance of two peaks to be merged. |
| mz_binning_width_unit | string | Da | Da, ppm | Unit in which the distance between two peaks is given. |
| sort_blocks | string | RT_ascending | RT_ascending, RT_descending | Sort blocks by before merging them (useful for precursor order) |
| 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 | min: 0 max: 100000000000 | Maximum RT size of the block in seconds (0.0 = no size restriction). |
| precursor_method:mz_tolerance | float | 0.0001 | min: 0 | Max m/z distance of the precursor entries of two spectra to be merged in [Da]. |
| precursor_method:rt_tolerance | float | 5 | min: 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
| 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 | ( | ) |
default constructor
| SpectraMerger | ( | const SpectraMerger & | source | ) |
copy constructor
| virtual ~SpectraMerger | ( | ) | [virtual] |
destructor
Member Function Documentation
| 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 SpectrumAlignment::getSpectrumAlignment(), LOG_INFO, DefaultParamHandler::setParameters(), and Param::setValue().
| void mergeSpectraBlockWise | ( | MapType & | exp | ) | [inline] |
| void mergeSpectraPrecursors | ( | MapType & | exp | ) | [inline] |
merges spectra with similar precursors (must have MS2 level)
References ClusterHierarchical::cluster(), ClusterAnalyzer::cut(), LOG_WARN, Peak2D::setMZ(), DefaultParamHandler::setParameters(), and Peak2D::setRT().
| SpectraMerger& operator= | ( | const SpectraMerger & | source | ) |
assignment operator
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:53 using doxygen 1.7.1 |