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... | |
![]() | |
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... | |
![]() | |
LogType | type_ |
SignedSize | begin_ |
SignedSize | end_ |
SignedSize | value_ |
QProgressDialog * | dlg_ |
StopWatch | stop_watch_ |
time_t | last_invoke_ |
Additional Inherited Members | |
![]() | |
enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
![]() | |
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 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.
|
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 |