78 std::vector<String> getLabels()
const;
80 double getScore()
const;
82 void setScore(
const double& score);
88 std::vector<double> getAllIntensities(
bool smoothed =
false)
const;
90 std::vector<double> getAllCentroidMZ()
const;
92 std::vector<double> getAllCentroidRT()
const;
94 std::vector<double> getIsotopeDistances()
const;
96 double getCentroidMZ()
const;
98 double getCentroidRT()
const;
100 double getFWHM()
const;
104 double getMonoisotopicFeatureIntensity(
bool)
const;
105 double getSummedFeatureIntensity(
bool)
const;
107 Size getNumFeatPoints()
const;
108 std::vector<ConvexHull2D> getConvexHulls()
const;
109 std::vector< OpenMS::MSChromatogram > getChromatograms(
UInt64 feature_id)
const;
189 void run(std::vector<MassTrace>& input_mtraces,
FeatureMap& output_featmap, std::vector<std::vector< OpenMS::MSChromatogram > >& output_chromatograms);
192 void updateMembers_()
override;
200 std::vector<const Element*> elementsFromString_(
const std::string& elements_string)
const;
208 Range getTheoreticIsotopicMassWindow_(
const std::vector<Element const *> alphabet,
int peakOffset)
const;
218 double computeCosineSim_(
const std::vector<double>&,
const std::vector<double>&)
const;
234 void loadIsotopeModel_(
const String&);
269 double scoreMZByExpectedMean_(
Size iso_pos,
Size charge,
const double diff_mz,
double mt_variances)
const;
279 double scoreMZByExpectedRange_(
Size charge,
const double diff_mz,
double mt_variances,
Range isotope_window)
const;
301 double computeAveragineSimScore_(
const std::vector<double>& intensities,
const double& molecular_weight)
const;
311 void findLocalFeatures_(
const std::vector<const MassTrace*>& candidates,
double total_intensity, std::vector<FeatureHypothesis>& output_hypotheses)
const;
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
double local_rt_range_
parameter stuff
Definition: FeatureFindingMetabo.h:321
double feat_score_
Definition: FeatureFindingMetabo.h:116
bool use_mz_scoring_by_element_range_
Definition: FeatureFindingMetabo.h:333
std::vector< double > svm_feat_scales_
Definition: FeatureFindingMetabo.h:316
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
svm_model * isotope_filt_svm_
SVM parameters.
Definition: FeatureFindingMetabo.h:314
A container type that gathers peaks similar in m/z and moving along retention time.
Definition: MassTrace.h:61
String isotope_filtering_model_
Definition: FeatureFindingMetabo.h:329
double local_mz_range_
Definition: FeatureFindingMetabo.h:322
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
bool report_summed_ints_
Definition: FeatureFindingMetabo.h:327
Internal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope gro...
Definition: FeatureFindingMetabo.h:58
double getCentroidMZ() const
Returns the centroid m/z.
Definition: MassTrace.h:179
double chrom_fwhm_
Definition: FeatureFindingMetabo.h:325
A container for features.
Definition: FeatureMap.h:95
double total_intensity_
Definition: FeatureFindingMetabo.h:318
std::vector< double > svm_feat_centers_
Definition: FeatureFindingMetabo.h:315
Size charge_upper_bound_
Definition: FeatureFindingMetabo.h:324
bool report_convex_hulls_
Definition: FeatureFindingMetabo.h:334
Size charge_lower_bound_
Definition: FeatureFindingMetabo.h:323
bool operator()(const MassTrace &x, const MassTrace &y) const
Definition: FeatureFindingMetabo.h:125
double left_boundary
Definition: FeatureFindingMetabo.h:148
bool enable_RT_filtering_
Definition: FeatureFindingMetabo.h:328
double right_boundary
Definition: FeatureFindingMetabo.h:149
bool report_chromatograms_
Definition: FeatureFindingMetabo.h:335
bool use_mz_scoring_C13_
Definition: FeatureFindingMetabo.h:332
Definition: FeatureFindingMetabo.h:132
Internal structure to store a lower and upper bound of an m/z range.
Definition: FeatureFindingMetabo.h:146
bool remove_single_traces_
Definition: FeatureFindingMetabo.h:337
bool use_smoothed_intensities_
Definition: FeatureFindingMetabo.h:330
SignedSize charge_
Definition: FeatureFindingMetabo.h:118
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
Method for the assembly of mass traces belonging to the same isotope pattern, i.e., that are compatible in retention times, mass-to-charge ratios, and isotope abundances.
Definition: FeatureFindingMetabo.h:177
Definition: FeatureFindingMetabo.h:121
A more convenient string class.
Definition: String.h:58
bool operator()(const FeatureHypothesis &x, const FeatureHypothesis &y) const
Definition: FeatureFindingMetabo.h:136
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
std::vector< const Element * > elements_
Definition: FeatureFindingMetabo.h:338
std::vector< const MassTrace * > iso_pattern_
Definition: FeatureFindingMetabo.h:114
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46