#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPicked.h>
FeatureFinderAlgorithmPicked Parameters are explained on a separate page.
Public Types | |
Type definitions | |
typedef FeatureFinderAlgorithm < PeakType, FeatureType > ::MapType | MapType |
Input map type. | |
typedef MapType::SpectrumType | SpectrumType |
typedef PeakType::CoordinateType | CoordinateType |
Coordinate/Position type of peaks. | |
typedef PeakType::IntensityType | IntensityType |
Intensity type of peaks. | |
Public Member Functions | |
FeatureFinderAlgorithmPicked () | |
default constructor | |
virtual void | run () |
Main method for actual FeatureFinder. | |
Static Public Member Functions | |
static FeatureFinderAlgorithm < PeakType, FeatureType > * | create () |
static const String | getProductName () |
Protected Member Functions | |
virtual void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParam() method. | |
void | abort_ (const String &reason) |
Writes the abort reason to the log file and counts occurences for each reason. | |
DoubleReal | intersection_ (const Feature &f1, const Feature &f2) |
const TheoreticalIsotopePattern & | getIsotopeDistribution_ (DoubleReal mass) |
Returns the isotope distribution for a certain mass window. | |
DoubleReal | findBestIsotopeFit_ (const Seed ¢er, UInt charge, IsotopePattern &best_pattern) |
Finds the best fitting position of the isotopic pattern estimate defined by center . | |
void | extendMassTraces_ (const IsotopePattern &pattern, MassTraces &traces) |
Extends all mass traces of a isotope pattern in one step. | |
void | extendMassTrace_ (MassTrace &trace, Int spectrum_index, DoubleReal mz, bool inc_rt, DoubleReal min_rt=0.0, DoubleReal max_rt=0.0) |
Extends a single mass trace in one RT direction. | |
template<typename SpectrumType> | |
UInt | nearest_ (CoordinateType pos, const SpectrumType &spec, UInt start) const |
Returns the index of the peak nearest to m/z pos in spectrum spec (linear search starting from index start ). | |
void | findIsotope_ (CoordinateType pos, UInt spectrum_index, IsotopePattern &pattern, UInt pattern_index, bool debug, UInt &peak_index) |
Searches for an isotopic peak in the current spectrum and the adjacent spectra. | |
DoubleReal | positionScore_ (CoordinateType pos1, CoordinateType pos2, DoubleReal allowed_deviation) const |
Calculates a score between 0 and 1 for the m/z deviation of two peaks. | |
DoubleReal | isotopeScore_ (const TheoreticalIsotopePattern &isotopes, IsotopePattern &pattern, bool consider_mz_distances, bool debug) |
Calculates a score between 0 and 1 for the correlation between theoretical and found isotope pattern. | |
DoubleReal | intensityScore_ (DoubleReal intensity, UInt spectrum, UInt peak) |
DoubleReal | intensityScore_ (UInt rt_bin, UInt mz_bin, DoubleReal intensity) |
Static Protected Member Functions | |
static int | gaussF_ (const gsl_vector *param, void *data, gsl_vector *f) |
static int | gaussDF_ (const gsl_vector *param, void *data, gsl_matrix *J) |
static int | gaussFDF_ (const gsl_vector *param, void *data, gsl_vector *f, gsl_matrix *J) |
Protected Attributes | |
std::ofstream | log_ |
Output stream for log/debug info. | |
std::map< String, UInt > | aborts_ |
Array of abort reasons. | |
std::vector< std::vector < PeakInfo > > | info_ |
Precalculated information for each peak. | |
std::vector < TheoreticalIsotopePattern > | isotope_distributions_ |
Vector of precalculated isotope distributions for several mass winows. | |
Members for parameters often needed in methods | |
DoubleReal | pattern_tolerance_ |
Stores mass_trace:mz_tolerance. | |
DoubleReal | trace_tolerance_ |
Stores isotopic_pattern:mz_tolerance. | |
UInt | min_spectra_ |
Number of spectra that have to show the same mass (for finding a mass trace). | |
UInt | max_missing_trace_peaks_ |
Stores mass_trace:max_missing. | |
DoubleReal | slope_bound_ |
Max slope of mass trace intensities. | |
DoubleReal | intensity_percentage_ |
Isotope pattern intensity contribution of required peaks. | |
DoubleReal | intensity_percentage_optional_ |
Isotope pattern intensity contribution of optional peaks. | |
DoubleReal | optional_fit_improvement_ |
Minimal imrovment for leaving out optional isotope. | |
DoubleReal | mass_window_width_ |
Width of the isotope pattern mass bins. | |
UInt | intensity_bins_ |
Number of bins (in RT and MZ) for intensity significance estimation. | |
DoubleReal | min_isotope_fit_ |
Mimimum isotope pattern fit for a feature. | |
DoubleReal | min_trace_score_ |
Minimum quality of a traces. | |
Members for intensity significance estimation | |
DoubleReal | intensity_rt_step_ |
RT bin width. | |
DoubleReal | intensity_mz_step_ |
m/z bin width | |
std::vector< std::vector < std::vector< DoubleReal > > > | intensity_thresholds_ |
Precalculated intensity 20-quantiles (binned). | |
Private Member Functions | |
FeatureFinderAlgorithmPicked & | operator= (const FeatureFinderAlgorithmPicked &) |
Not implemented. | |
FeatureFinderAlgorithmPicked (const FeatureFinderAlgorithmPicked &) | |
Not implemented. | |
Classes | |
struct | IsotopePattern |
Helper structure for a found isotope pattern used in FeatureFinderAlgorithmPicked. More... | |
struct | MassTrace |
Helper struct for mass traces used in FeatureFinderAlgorithmPicked. More... | |
struct | MassTraces |
Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked. More... | |
struct | PeakInfo |
Helper structure that stores precalculated information for each peak used in FeatureFinderAlgorithmPicked. More... | |
struct | Seed |
Helper structure for seeds used in FeatureFinderAlgorithmPicked. More... | |
struct | TheoreticalIsotopePattern |
Helper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked. More... |
typedef FeatureFinderAlgorithm<PeakType, FeatureType>::MapType MapType |
typedef MapType::SpectrumType SpectrumType |
typedef PeakType::IntensityType IntensityType |
FeatureFinderAlgorithmPicked | ( | ) | [inline] |
default constructor
FeatureFinderAlgorithmPicked | ( | const FeatureFinderAlgorithmPicked< PeakType, FeatureType > & | ) | [private] |
Not implemented.
virtual void run | ( | ) | [inline, virtual] |
static FeatureFinderAlgorithm<PeakType,FeatureType>* create | ( | ) | [inline, static] |
static const String getProductName | ( | ) | [inline, static] |
virtual void updateMembers_ | ( | ) | [inline, protected, virtual] |
This method is used to update extra member variables at the end of the setParam() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from DefaultParamHandler.
void abort_ | ( | const String & | reason | ) | [inline, protected] |
Writes the abort reason to the log file and counts occurences for each reason.
DoubleReal intersection_ | ( | const Feature & | f1, | |
const Feature & | f2 | |||
) | [inline, protected] |
Calculates the intersection between features. The value is normalized by the size of the smaller feature, so it rages from 0 to 1.
const TheoreticalIsotopePattern& getIsotopeDistribution_ | ( | DoubleReal | mass | ) | [inline, protected] |
Returns the isotope distribution for a certain mass window.
DoubleReal findBestIsotopeFit_ | ( | const Seed & | center, | |
UInt | charge, | |||
IsotopePattern & | best_pattern | |||
) | [inline, protected] |
Finds the best fitting position of the isotopic pattern estimate defined by center
.
center | the maximum peak of the isotope distribution (contains charge as well) | |
charge | The charge of the pattern | |
best_pattern | Returns the indices of the isotopic peaks. If a isopopic peak is missing -1 is returned. |
void extendMassTraces_ | ( | const IsotopePattern & | pattern, | |
MassTraces & | traces | |||
) | [inline, protected] |
Extends all mass traces of a isotope pattern in one step.
void extendMassTrace_ | ( | MassTrace & | trace, | |
Int | spectrum_index, | |||
DoubleReal | mz, | |||
bool | inc_rt, | |||
DoubleReal | min_rt = 0.0 , |
|||
DoubleReal | max_rt = 0.0 | |||
) | [inline, protected] |
Extends a single mass trace in one RT direction.
How to use this method:
trace
UInt nearest_ | ( | CoordinateType | pos, | |
const SpectrumType & | spec, | |||
UInt | start | |||
) | const [inline, protected] |
Returns the index of the peak nearest to m/z pos
in spectrum spec
(linear search starting from index start
).
void findIsotope_ | ( | CoordinateType | pos, | |
UInt | spectrum_index, | |||
IsotopePattern & | pattern, | |||
UInt | pattern_index, | |||
bool | debug, | |||
UInt & | peak_index | |||
) | [inline, protected] |
Searches for an isotopic peak in the current spectrum and the adjacent spectra.
pos | m/z position of the searched for peak | |
spectrum_index | index of the central spectrum | |
pattern | IsotopePattern to store found peaks | |
pattern_index | index of the isotope in the pattern | |
debug | Flag that turn on debug info | |
peak_index | starting index of the search (to avoid multiple binary searches) |
DoubleReal positionScore_ | ( | CoordinateType | pos1, | |
CoordinateType | pos2, | |||
DoubleReal | allowed_deviation | |||
) | const [inline, protected] |
Calculates a score between 0 and 1 for the m/z deviation of two peaks.
DoubleReal isotopeScore_ | ( | const TheoreticalIsotopePattern & | isotopes, | |
IsotopePattern & | pattern, | |||
bool | consider_mz_distances, | |||
bool | debug | |||
) | [inline, protected] |
Calculates a score between 0 and 1 for the correlation between theoretical and found isotope pattern.
DoubleReal intensityScore_ | ( | DoubleReal | intensity, | |
UInt | spectrum, | |||
UInt | peak | |||
) | [inline, protected] |
DoubleReal intensityScore_ | ( | UInt | rt_bin, | |
UInt | mz_bin, | |||
DoubleReal | intensity | |||
) | [inline, protected] |
static int gaussF_ | ( | const gsl_vector * | param, | |
void * | data, | |||
gsl_vector * | f | |||
) | [inline, static, protected] |
static int gaussDF_ | ( | const gsl_vector * | param, | |
void * | data, | |||
gsl_matrix * | J | |||
) | [inline, static, protected] |
static int gaussFDF_ | ( | const gsl_vector * | param, | |
void * | data, | |||
gsl_vector * | f, | |||
gsl_matrix * | J | |||
) | [inline, static, protected] |
FeatureFinderAlgorithmPicked& operator= | ( | const FeatureFinderAlgorithmPicked< PeakType, FeatureType > & | ) | [private] |
Not implemented.
std::ofstream log_ [protected] |
Output stream for log/debug info.
DoubleReal pattern_tolerance_ [protected] |
Stores mass_trace:mz_tolerance.
DoubleReal trace_tolerance_ [protected] |
Stores isotopic_pattern:mz_tolerance.
UInt min_spectra_ [protected] |
Number of spectra that have to show the same mass (for finding a mass trace).
UInt max_missing_trace_peaks_ [protected] |
Stores mass_trace:max_missing.
DoubleReal slope_bound_ [protected] |
Max slope of mass trace intensities.
DoubleReal intensity_percentage_ [protected] |
Isotope pattern intensity contribution of required peaks.
DoubleReal intensity_percentage_optional_ [protected] |
Isotope pattern intensity contribution of optional peaks.
DoubleReal optional_fit_improvement_ [protected] |
Minimal imrovment for leaving out optional isotope.
DoubleReal mass_window_width_ [protected] |
Width of the isotope pattern mass bins.
UInt intensity_bins_ [protected] |
Number of bins (in RT and MZ) for intensity significance estimation.
DoubleReal min_isotope_fit_ [protected] |
Mimimum isotope pattern fit for a feature.
DoubleReal min_trace_score_ [protected] |
Minimum quality of a traces.
DoubleReal intensity_rt_step_ [protected] |
RT bin width.
DoubleReal intensity_mz_step_ [protected] |
m/z bin width
std::vector< std::vector< std::vector<DoubleReal> > > intensity_thresholds_ [protected] |
Precalculated intensity 20-quantiles (binned).
std::vector< TheoreticalIsotopePattern > isotope_distributions_ [protected] |
Vector of precalculated isotope distributions for several mass winows.
Generated Tue Apr 1 15:36:47 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |