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FeatureFinder Class Reference

The main feature finder class. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinder.h>

Inheritance diagram for FeatureFinder:
ProgressLogger FeatureFinderDefs

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 &param, const FeatureMap< FeatureType > &seeds)
 Executes the FeatureFinder using the given algorithm. More...
 
const FlaggetPeakFlag (const IndexPair &index) const
 Returns a non-mutable reference to a peak flag. More...
 
FlaggetPeakFlag (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_
 

Detailed Description

The main feature finder class.

Constructor & Destructor Documentation

Default constructor.

virtual ~FeatureFinder ( )
virtual

Destructor.

Member Function Documentation

Param getParameters ( const String algorithm_name) const

Returns the default parameters for the algorithm with name algorithm_name.

const Flag& getPeakFlag ( const IndexPair index) const
inline
Flag& getPeakFlag ( const IndexPair index)
inline

Returns mutable reference to a peak flag.

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_nameName of the feature finding algorithm to use
input_mapInput peak map
featuresOutput feature map
paramAlgorithm parameters
seedsList of seeds to use

Implemented in FeatureFinder_impl.h

Todo:
that happens sometimes using IsotopeWaveletFeatureFinder (Rene, Marc, Andreas, Clemens)

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.

Member Data Documentation

std::vector<std::vector<Flag> > flags_
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