Simple seeding class that uses the strongest peak as next seed. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SimpleSeeder.h>
Public Types | |
typedef FeaFiModule< PeakType, FeatureType > | Base |
typedef MSExperiment< PeakType > | MapType |
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typedef FeatureMap< FeatureType > | FeatureMapType |
Output feature map type. More... | |
typedef MSExperiment< PeakType > | MapType |
Input map type. More... | |
typedef MapType::SpectrumType | SpectrumType |
Input spectrum type. More... | |
typedef PeakType::IntensityType | IntensityType |
Input intensity type. More... | |
typedef PeakType::CoordinateType | CoordinateType |
Input coordinate type. More... | |
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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... | |
Public Member Functions | |
SimpleSeeder (const MSExperiment< PeakType > *map, FeatureMap< FeatureType > *features, FeatureFinder *ff) | |
Constructor. More... | |
virtual | ~SimpleSeeder () |
destructor More... | |
IndexPair | nextSeed () |
return the next seed More... | |
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FeaFiModule (const MSExperiment< PeakType > *map, FeatureMap< FeatureType > *features, FeatureFinder *ff) | |
Constructor. More... | |
virtual | ~FeaFiModule () |
destructor More... | |
IntensityType | getPeakIntensity (const FeatureFinderDefs::IndexPair &index) const |
Returns the intensity of a peak. More... | |
CoordinateType | getPeakMz (const FeatureFinderDefs::IndexPair &index) const |
Returns the m/z of a peak. More... | |
CoordinateType | getPeakRt (const FeatureFinderDefs::IndexPair &index) const |
Returns the retention time of a peak. More... | |
void | getNextMz (FeatureFinderDefs::IndexPair &index) const |
fills index with the index of next peak in m/z dimension More... | |
void | getPrevMz (FeatureFinderDefs::IndexPair &index) const |
fills index with the index of previous peak in m/z dimension More... | |
void | getNextRt (FeatureFinderDefs::IndexPair &index) |
fills index with the index of the nearest peak in the next scan More... | |
void | getPrevRt (FeatureFinderDefs::IndexPair &index) |
fills index with the index of the nearest peak in the previous scan More... | |
void | addConvexHull (const FeatureFinderDefs::IndexSet &set, Feature &feature) const |
Calculates the convex hull of a index set and adds it to the feature . More... | |
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DefaultParamHandler (const String &name) | |
Constructor with name that is displayed in error messages. More... | |
DefaultParamHandler (const DefaultParamHandler &rhs) | |
Copy constructor. More... | |
virtual | ~DefaultParamHandler () |
Destructor. More... | |
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () const |
Non-mutable access to the name. More... | |
void | setName (const String &name) |
Mutable access to the name. More... | |
const std::vector< String > & | getSubsections () const |
Non-mutable access to the registered subsections. More... | |
Protected Member Functions | |
void | initialize_ () |
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virtual void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
std::vector< IndexPair > | indices_ |
contains the indizes More... | |
std::vector< IndexPair > ::const_iterator | current_peak_ |
Points to the next peak in the peak vector. More... | |
bool | initialized_ |
Flag that indicates of the indices are initialized. More... | |
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const MapType * | map_ |
Input data pointer. More... | |
FeatureMapType * | features_ |
Output data pointer. More... | |
FeatureFinder * | ff_ |
Pointer to the calling FeatureFinder that is used to access the feature flags and report progress. More... | |
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Param | param_ |
Container for current parameters. More... | |
Param | defaults_ |
Container for default parameters. This member should be filled in the constructor of derived classes! More... | |
std::vector< String > | subsections_ |
Container for registered subsections. This member should be filled in the constructor of derived classes! More... | |
String | error_name_ |
Name that is displayed in error messages during the parameter checking. More... | |
bool | check_defaults_ |
If this member is set to false no checking if parameters in done;. More... | |
bool | warn_empty_defaults_ |
If this member is set to false no warning is emitted when defaults are empty;. More... | |
Private Member Functions | |
SimpleSeeder () | |
Not implemented. More... | |
SimpleSeeder & | operator= (const SimpleSeeder &) |
Not implemented. More... | |
SimpleSeeder (const SimpleSeeder &) | |
Not implemented. More... | |
Simple seeding class that uses the strongest peak as next seed.
This class simply sorts the peaks according to intensity and proposes the highest peak, which is not yet included in a feature, as next seed.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
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min_intensity | float | 0 | min: 0 | Absolute value for the minimum intensity required for a seed. |
signal_to_noise | float | 10 | min: 0 | Minimal required SignalToNoise (S/N) ratio for a seed. |
SignalToNoiseEstimationParameter:max_intensity | int | -1 | min: -1 | maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N. |
SignalToNoiseEstimationParameter:auto_max_stdev_factor | float | 3 | min: 0 max: 999 | parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev |
SignalToNoiseEstimationParameter:auto_max_percentile | int | 95 | min: 0 max: 100 | parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile |
SignalToNoiseEstimationParameter:auto_mode | int | 0 | min: -1 max: 1 | method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method |
SignalToNoiseEstimationParameter:win_len | float | 200 | min: 1 | window length in Thomson |
SignalToNoiseEstimationParameter:bin_count | int | 30 | min: 3 | number of bins for intensity values |
SignalToNoiseEstimationParameter:min_required_elements | int | 10 | min: 1 | minimum number of elements required in a window (otherwise it is considered sparse) |
SignalToNoiseEstimationParameter:noise_for_empty_window | float | 1e+20 | noise value used for sparse windows |
typedef FeaFiModule<PeakType, FeatureType> Base |
typedef MSExperiment<PeakType> MapType |
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inline |
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inlinevirtual |
destructor
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private |
Not implemented.
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private |
Not implemented.
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inlineprotected |
References Param::copy(), SimpleSeeder< PeakType, FeatureType >::current_peak_, FeaFiModule< PeakType, FeatureType >::ff_, FeaFiModule< PeakType, FeatureType >::getPeakIntensity(), SignalToNoiseEstimator< Container >::getSignalToNoise(), Param::getValue(), SimpleSeeder< PeakType, FeatureType >::indices_, SignalToNoiseEstimator< Container >::init(), SimpleSeeder< PeakType, FeatureType >::initialized_, FeaFiModule< PeakType, FeatureType >::map_, DefaultParamHandler::param_, OpenMS::reverseComparator(), DefaultParamHandler::setParameters(), and ProgressLogger::startProgress().
Referenced by SimpleSeeder< PeakType, FeatureType >::nextSeed().
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inline |
return the next seed
References SimpleSeeder< PeakType, FeatureType >::current_peak_, FeaFiModule< PeakType, FeatureType >::ff_, FeatureFinder::getPeakFlag(), SimpleSeeder< PeakType, FeatureType >::indices_, SimpleSeeder< PeakType, FeatureType >::initialize_(), SimpleSeeder< PeakType, FeatureType >::initialized_, ProgressLogger::setProgress(), and FeatureFinderDefs::USED.
Referenced by FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmSimple< PeakType, FeatureType >::run().
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private |
Not implemented.
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protected |
Points to the next peak in the peak vector.
Referenced by SimpleSeeder< PeakType, FeatureType >::initialize_(), and SimpleSeeder< PeakType, FeatureType >::nextSeed().
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protected |
contains the indizes
Referenced by SimpleSeeder< PeakType, FeatureType >::initialize_(), and SimpleSeeder< PeakType, FeatureType >::nextSeed().
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protected |
Flag that indicates of the indices are initialized.
Referenced by SimpleSeeder< PeakType, FeatureType >::initialize_(), and SimpleSeeder< PeakType, FeatureType >::nextSeed().
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5 |