The main feature finder class. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinder.h>
Public Member Functions | |
| FeatureFinder () | |
| Default constructor. | |
| virtual | ~FeatureFinder () |
| Destructor. | |
| template<class PeakType , class FeatureType > | |
| void | run (const String &algorithm_name, MSExperiment< PeakType > &input_map, FeatureMap< FeatureType > &features, const Param ¶m, const FeatureMap< FeatureType > &seeds) |
| Executes the FeatureFinder using the given algorithm. | |
| const Flag & | getPeakFlag (const IndexPair &index) const |
| Returns a non-mutable reference to a peak flag. | |
| Flag & | getPeakFlag (const IndexPair &index) |
| Returns mutable reference to a peak flag. | |
| Param | getParameters (const String &algorithm_name) const |
Returns the default parameters for the algorithm with name algorithm_name. | |
Protected Attributes | |
| std::vector< std::vector< Flag > > | flags_ |
| Container for flags attached to input data. | |
Detailed Description
The main feature finder class.
- Stores the flags for (indices of) data points ("used", "unused")
- The algorithm itself is a factory product (derived from FeatureFinderAlgorithm)
- The main method is run(), which is a template so that we can deal with different types of input and output
- The run() method takes five arguments: algorithm_name, input_map, output, parameters, seeds
Constructor & Destructor Documentation
| FeatureFinder | ( | ) |
Default constructor.
| virtual ~FeatureFinder | ( | ) | [virtual] |
Destructor.
Member Function Documentation
Returns the default parameters for the algorithm with name algorithm_name.
Returns a non-mutable reference to a peak flag.
Referenced by SimpleExtender< PeakType, FeatureType >::checkNeighbour_(), SimpleExtender< PeakType, FeatureType >::extend(), ModelFitter< PeakType, FeatureType >::fit(), SimpleSeeder< PeakType, FeatureType >::nextSeed(), FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmSimple< PeakType, FeatureType >::run().
| void run | ( | const String & | algorithm_name, | |
| MSExperiment< PeakType > & | input_map, | |||
| FeatureMap< FeatureType > & | features, | |||
| const Param & | param, | |||
| const FeatureMap< FeatureType > & | seeds | |||
| ) |
Executes the FeatureFinder using the given algorithm.
There are several constraints for the input_map. They are tested before the algorithm starts. It must only contain MS 1 level scans and you have to call updateRanges() before passing it to this method. The input map is sorted by RT & m/z if thats not the case. Furthermore we throw an Exception if the data contains negative m/z values, as this will disturb most algorithms.
- Parameters:
-
algorithm_name Name of the feature finding algorithm to use input_map Input peak map features Output feature map param Algorithm parameters seeds List of seeds to use
Implemented in FeatureFinder_impl.h
- Todo:
- that happens sometimes using IsotopeWaveletFeatureFinder (Rene, Marc, Andreas, Clemens)
References FeatureMap< FeatureT >::clear(), FeatureFinder::flags_, MSExperiment< PeakT, ChromatogramPeakT >::getChromatograms(), MSExperiment< PeakT, ChromatogramPeakT >::getMSLevels(), MSExperiment< PeakT, ChromatogramPeakT >::getSize(), MSExperiment< PeakT, ChromatogramPeakT >::isSorted(), LOG_WARN, MSExperiment< PeakT, ChromatogramPeakT >::RTBegin(), FeatureFinderAlgorithm< PeakType, FeatureType >::run(), FeatureFinderAlgorithm< PeakType, FeatureType >::setData(), DefaultParamHandler::setParameters(), FeatureFinderAlgorithm< PeakType, FeatureType >::setSeeds(), MSExperiment< PeakT, ChromatogramPeakT >::sortChromatograms(), MSExperiment< PeakT, ChromatogramPeakT >::sortSpectra(), and FeatureFinderDefs::UNUSED.
Member Data Documentation
Container for flags attached to input data.
Referenced by FeatureFinder::run().
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1 |