37 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_SIMPLESEEDER_H
38 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SIMPLESEEDER_H
60 template <
class PeakType,
class FeatureType>
71 Base(map, features, ff),
76 this->
defaults_.
setValue(
"min_intensity", 0.0,
"Absolute value for the minimum intensity required for a seed.");
78 this->
defaults_.
setValue(
"signal_to_noise", 10.0,
"Minimal required SignalToNoise (S/N) ratio for a seed.");
127 typename FeatureType::IntensityType noise_threshold = this->
param_.
getValue(
"min_intensity");
128 typename FeatureType::IntensityType sn = this->
param_.
getValue(
"signal_to_noise");
130 #ifdef DEBUG_FEATUREFINDER
131 std::cout <<
"Intensity threshold: " << noise_threshold << std::endl;
132 std::cout <<
"S/N: " << sn << std::endl;
139 while (tmp.first < (*this->map_).size())
142 while (tmp.second < (*this->map_)[tmp.first].size())
156 Param param(this->
param_.
copy(
"SignalToNoiseEstimationParameter:",
true));
161 estimator.
init(it->begin(), it->end());
175 #ifdef DEBUG_FEATUREFINDER
176 std::cout <<
"Number of peaks above threshold (" << noise_threshold <<
") and S/N (" << sn <<
"): " <<
indices_.size() << std::endl;
213 #endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SIMPLESEEDER_H
virtual double getSignalToNoise(const PeakIterator &data_point)
Definition: SignalToNoiseEstimator.h:130
Implements a module of the FeatureFinder algorithm.
Definition: FeaFiModule.h:157
void initialize_()
Definition: SimpleSeeder.h:124
IsotopeCluster::IndexPair IndexPair
Index to peak consisting of two UInts (scan index / peak index)
Definition: FeatureFinderDefs.h:54
Definition: FeatureFinderDefs.h:63
Param defaults_
Container for default parameters. This member should be filled in the constructor of derived classes!...
Definition: DefaultParamHandler.h:155
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
const Param & getDefaults() const
Non-mutable access to the default parameters.
FeaFiModule< PeakType, FeatureType > Base
Definition: SimpleSeeder.h:66
void insert(const String &prefix, const Param ¶m)
IntensityType getPeakIntensity(const FeatureFinderDefs::IndexPair &index) const
Returns the intensity of a peak.
Definition: FeaFiModule.h:190
Param param_
Container for current parameters.
Definition: DefaultParamHandler.h:148
A container for features.
Definition: FeatureMap.h:111
MSExperiment< PeakType > MapType
Definition: SimpleSeeder.h:67
ReverseComparator< Cmp > reverseComparator(Cmp const &cmp)
Make-function to create a ReverseComparator from another comparator without the need to specify the t...
Definition: ComparatorUtils.h:261
IndexPair nextSeed()
return the next seed
Definition: SimpleSeeder.h:94
void setParameters(const Param ¶m)
Sets the parameters.
FeatureFinder * ff_
Pointer to the calling FeatureFinder that is used to access the feature flags and report progress...
Definition: FeaFiModule.h:415
The purpose of this struct is to provide definitions of classes and typedefs which are used throughou...
Definition: FeatureFinderDefs.h:51
const MapType * map_
Input data pointer.
Definition: FeaFiModule.h:411
SimpleSeeder & operator=(const SimpleSeeder &)
Not implemented.
std::vector< IndexPair >::const_iterator current_peak_
Points to the next peak in the peak vector.
Definition: SimpleSeeder.h:196
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
SimpleSeeder()
Not implemented.
virtual void init(const PeakIterator &it_begin, const PeakIterator &it_end)
Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimat...
Definition: SignalToNoiseEstimator.h:111
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
virtual ~SimpleSeeder()
destructor
Definition: SimpleSeeder.h:89
Comparator that allows to compare the indices of two peaks by their intensity.
Definition: FeaFiModule.h:56
Exception that is thrown if a method an invalid IndexPair is given.
Definition: FeatureFinderDefs.h:66
bool initialized_
Flag that indicates of the indices are initialized.
Definition: SimpleSeeder.h:199
Management and storage of parameters / INI files.
Definition: Param.h:69
Representation of a mass spectrometry experiment.
Definition: MSExperiment.h:68
SimpleSeeder(const MSExperiment< PeakType > *map, FeatureMap< FeatureType > *features, FeatureFinder *ff)
Constructor.
Definition: SimpleSeeder.h:70
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:103
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
void setProgress(SignedSize value) const
Sets the current progress.
std::vector< IndexPair > indices_
contains the indizes
Definition: SimpleSeeder.h:193
The main feature finder class.
Definition: FeatureFinder.h:57
void setName(const String &name)
Mutable access to the name.
const Flag & getPeakFlag(const IndexPair &index) const
Returns a non-mutable reference to a peak flag.
Definition: FeatureFinder.h:91
Simple seeding class that uses the strongest peak as next seed.
Definition: SimpleSeeder.h:61
void setMinFloat(const String &key, DoubleReal min)
Sets the minimum value for the floating point or floating point list parameter key.
void defaultsToParam_()
Updates the parameters after the defaults have been set in the constructor.