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))  More... | |
| Public Member Functions | |
| SpectraMerger () | |
| default constructor  More... | |
| SpectraMerger (const SpectraMerger &source) | |
| copy constructor  More... | |
| virtual | ~SpectraMerger () | 
| 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... | |
|  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 ¶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... | |
| 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... | |
|  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... | |
| 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... | |
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]. | 
| typedef Map<Size, std::vector<Size> > MergeBlocks | 
blocks of spectra (master-spectrum index to sacrifice-spectra(the ones being merged into the master-spectrum))
| SpectraMerger | ( | ) | 
default constructor
| SpectraMerger | ( | const SpectraMerger & | source | ) | 
copy constructor
| 
 | virtual | 
destructor
| 
 | inlineprotected | 
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().
| 
 | inline | 
| 
 | 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 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:30 using doxygen 1.8.5 |