The main feature finder class. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinder.h>
Public Member Functions | |
| FeatureFinder () | |
| Default constructor. More... | |
| virtual | ~FeatureFinder () |
| Destructor. More... | |
| 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. More... | |
| const Flag & | getPeakFlag (const IndexPair &index) const |
| Returns a non-mutable reference to a peak flag. More... | |
| Flag & | getPeakFlag (const IndexPair &index) |
| Returns mutable reference to a peak flag. More... | |
| Param | getParameters (const String &algorithm_name) const |
Returns the default parameters for the algorithm with name algorithm_name. More... | |
Public Member Functions inherited from ProgressLogger | |
| ProgressLogger () | |
| Constructor. More... | |
| ~ProgressLogger () | |
| Destructor. 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... | |
Protected Attributes | |
| std::vector< std::vector< Flag > > | flags_ |
| Container for flags attached to input data. More... | |
Protected Attributes inherited from ProgressLogger | |
| LogType | type_ |
| SignedSize | begin_ |
| SignedSize | end_ |
| SignedSize | value_ |
| QProgressDialog * | dlg_ |
| StopWatch | stop_watch_ |
| time_t | last_invoke_ |
Additional Inherited Members | |
Public Types inherited from ProgressLogger | |
| enum | LogType { CMD, GUI, NONE } |
| Possible log types. More... | |
Public Types inherited from FeatureFinderDefs | |
| enum | Flag { UNUSED, USED } |
| Flags that indicate if a peak is already used in a feature. More... | |
| typedef IsotopeCluster::IndexPair | IndexPair |
| Index to peak consisting of two UInts (scan index / peak index) More... | |
| typedef IsotopeCluster::ChargedIndexSet | ChargedIndexSet |
| Index to peak consisting of two UInts (scan index / peak index) with charge information. More... | |
| typedef IsotopeCluster::IndexSet | IndexSet |
| A set of peak indices. More... | |
Static Protected Attributes inherited from ProgressLogger | |
| static int | recursion_depth_ |
The main feature finder class.
| FeatureFinder | ( | ) |
Default constructor.
|
virtual |
Destructor.
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.
| 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
References MSExperiment< PeakT, ChromatogramPeakT >::begin(), FeatureMap< FeatureT >::clear(), MSExperiment< PeakT, ChromatogramPeakT >::empty(), 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 >::size(), MSExperiment< PeakT, ChromatogramPeakT >::sortChromatograms(), MSExperiment< PeakT, ChromatogramPeakT >::sortSpectra(), and FeatureFinderDefs::UNUSED.
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protected |
Container for flags attached to input data.
Referenced by FeatureFinder::run().
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5 |