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OpenMS
2.4.0
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48 #include <boost/shared_ptr.hpp>
49 #include <boost/make_shared.hpp>
80 use_coelution_score_(true),
81 use_shape_score_(true),
83 use_library_score_(true),
84 use_elution_model_score_(true),
85 use_intensity_score_(true),
86 use_total_xic_score_(true),
87 use_total_mi_score_(true),
88 use_nr_peaks_score_(true),
91 use_dia_scores_(true),
92 use_sonar_scores(true),
93 use_ms1_correlation(true),
94 use_ms1_fullscan(true),
178 elution_model_fit_score(0),
180 library_norm_manhattan(0),
181 library_rootmeansquare(0),
184 isotope_correlation(0),
185 ind_isotope_correlation(
""),
187 ind_isotope_overlap(
""),
189 ind_massdev_score(
""),
190 xcorr_coelution_score(0),
191 ind_xcorr_coelution_score(
""),
192 xcorr_shape_score(0),
193 ind_xcorr_shape_score(
""),
197 ind_log_sn_score(
""),
198 ind_num_transitions(0),
199 ind_transition_names(
""),
200 ind_area_intensity(
""),
201 ind_total_area_intensity(
""),
202 ind_intensity_score(
""),
203 ind_apex_intensity(
""),
205 ind_log_intensity(
""),
206 ind_intensity_ratio(
""),
208 weighted_coelution_score(0),
209 weighted_xcorr_shape(0),
210 weighted_massdev_score(0),
211 xcorr_ms1_coelution_score(0),
212 xcorr_ms1_shape_score(0),
214 ms1_isotope_correlation(0),
215 ms1_isotope_overlap(0),
223 library_manhattan(0),
231 weighted_mi_score(0),
232 dotprod_score_dia(0),
238 double get_quick_lda_score(
double library_corr_,
double library_norm_manhattan_,
double norm_rt_score_,
double xcorr_coelution_score_,
239 double xcorr_shape_score_,
double log_sn_score_)
const
253 double lda_quick_score =
254 library_corr_ * -0.5319046 +
255 library_norm_manhattan_ * 2.1643962 +
256 norm_rt_score_ * 8.0353047 +
257 xcorr_coelution_score_ * 0.1458914 +
258 xcorr_shape_score_ * -1.6901925 +
259 log_sn_score_ * -0.8002824;
260 return lda_quick_score;
503 void initialize(
double rt_normalization_factor,
505 double spacing_for_spectra_resampling,
525 void calculateChromatographicScores(
527 const std::vector<std::string>& native_ids,
528 const std::string& precursor_chrom_id,
529 const std::vector<double>& normalized_library_intensity,
530 std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators,
551 void calculateChromatographicIdScores(
553 const std::vector<std::string>& native_ids_identification,
554 const std::vector<std::string>& native_ids_detection,
555 std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators,
573 void calculateLibraryScores(
575 const std::vector<TransitionType> & transitions,
577 const double normalized_feature_rt,
594 const std::vector<TransitionType> & transitions,
595 std::vector<OpenSwath::SwathMap> swath_maps,
632 const std::vector<OpenSwath::SwathMap> swath_maps,
644 void getNormalized_library_intensities_(
const std::vector<TransitionType> & transitions,
645 std::vector<double>& normalized_library_intensity);
661 double RT,
int nr_spectra_to_add);
677 double RT,
int nr_spectra_to_add);
double massdev_score
Definition: OpenSwathScoring.h:121
double sonar_sn
Definition: OpenSwathScoring.h:153
bool use_rt_score_
Definition: OpenSwathScoring.h:63
OpenSwath::LightTransition TransitionType
Definition: OpenSwathScoring.h:478
double yseries_score
Definition: OpenSwathScoring.h:127
Size ensureUniqueId()
Assigns a valid unique id, but only if the present one is invalid. Returns 1 if the unique id was cha...
Definition: UniqueIdInterface.h:158
Base class for TOPP applications.
Definition: TOPPBase.h:150
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
std::string ind_total_area_intensity
Definition: OpenSwathScoring.h:134
std::string ind_massdev_score
Definition: OpenSwathScoring.h:122
bool use_total_xic_score_
Definition: OpenSwathScoring.h:67
PeakMap MapType
Definition: PeakPickerIterative.cpp:84
OpenSwath::LightCompound CompoundType
Definition: OpenSwathScoring.h:477
double log_sn_score
Definition: OpenSwathScoring.h:129
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
std::string ind_xcorr_coelution_score
Definition: OpenSwathScoring.h:124
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:83
double ms1_isotope_overlap
Definition: OpenSwathScoring.h:150
bool use_ms1_fullscan
Definition: OpenSwathScoring.h:75
int add_up_spectra_
Definition: OpenSwathScoring.h:481
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:93
double ms1_mi_score
Definition: OpenSwathScoring.h:151
OpenSwath_Scores_Usage su_
Definition: OpenSwathScoring.h:483
std::string ind_mi_score
Definition: OpenSwathScoring.h:167
bool use_dia_scores_
Definition: OpenSwathScoring.h:72
double sonar_diff
Definition: OpenSwathScoring.h:154
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
std::string ind_isotope_overlap
Definition: OpenSwathScoring.h:120
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:57
double manhatt_score_dia
Definition: OpenSwathScoring.h:175
void setValidStrings(const String &key, const std::vector< String > &strings)
Sets the valid strings for the parameter key.
double xcorr_coelution_score
Definition: OpenSwathScoring.h:123
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
void pickExperiment(PeakMap &chromatograms, FeatureMap &output, TargetedExperiment &transition_exp, TransformationDescription trafo, PeakMap &swath_map)
Picker and prepare functions.
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
double sonar_shape
Definition: OpenSwathScoring.h:157
std::string ind_intensity_score
Definition: OpenSwathScoring.h:135
double mi_score
Definition: OpenSwathScoring.h:166
std::string ind_xcorr_shape_score
Definition: OpenSwathScoring.h:126
bool use_nr_peaks_score_
Definition: OpenSwathScoring.h:69
double calculate_swath_lda_prescore(OpenSwath_Scores scores) const
Definition: OpenSwathScoring.h:299
bool use_elution_model_score_
Definition: OpenSwathScoring.h:65
void load(const String &filename, TargetedExperiment &id)
Loads a map from a TraML file.
bool use_mi_score_
Definition: OpenSwathScoring.h:71
double norm_rt_score
Definition: OpenSwathScoring.h:116
double calculate_lda_single_transition(OpenSwath_Scores scores) const
Definition: OpenSwathScoring.h:291
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
A structure to store which scores should be used by the Algorithm.
Definition: OpenSwathScoring.h:58
std::string ind_intensity_ratio
Definition: OpenSwathScoring.h:139
double library_norm_manhattan
Definition: OpenSwathScoring.h:113
double rt_normalization_factor_
Definition: OpenSwathScoring.h:480
Definition: TransitionExperiment.h:206
OpenSwath_Scores_Usage()
Definition: OpenSwathScoring.h:79
double xcorr_shape_score
Definition: OpenSwathScoring.h:125
double library_rootmeansquare
Definition: OpenSwathScoring.h:114
std::string ind_transition_names
Definition: OpenSwathScoring.h:132
static bool computeBinnedCoverage(const std::pair< double, double > &rtRange, const std::vector< std::pair< double, double > > &pairs, int nrBins, int minPeptidesPerBin, int minBinsFilled)
Computes coverage of the RT normalization peptides over the whole RT range, ensuring that each bin ha...
std::map< String, MRMTransitionGroupType > TransitionGroupMapType
Definition: MRMFeatureFinderScoring.h:109
static void convertTargetedExp(const OpenMS::TargetedExperiment &transition_exp_, OpenSwath::LightTargetedExperiment &transition_exp)
convert from the OpenMS TargetedExperiment to the LightTargetedExperiment
double rt_difference
Definition: OpenSwathScoring.h:170
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool toBool() const
Conversion to bool.
double library_corr
Definition: OpenSwathScoring.h:112
File adapter for HUPO PSI TraML files.
Definition: TraMLFile.h:63
Definition: TransitionExperiment.h:149
double bseries_score
Definition: OpenSwathScoring.h:128
double elution_model_fit_score
Definition: OpenSwathScoring.h:111
std::vector< LightCompound > & getCompounds()
Definition: TransitionExperiment.h:228
double nr_peaks
Definition: OpenSwathScoring.h:164
bool use_library_score_
Definition: OpenSwathScoring.h:64
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
double calculate_lda_prescore(OpenSwath_Scores scores) const
Definition: OpenSwathScoring.h:263
double spacing_for_spectra_resampling_
Definition: OpenSwathScoring.h:482
static std::vector< std::pair< double, double > > removeOutliersRANSAC(const std::vector< std::pair< double, double > > &pairs, double rsq_limit, double coverage_limit, size_t max_iterations, double max_rt_threshold, size_t sampling_size)
This function removes potential outliers in a linear regression dataset.
double weighted_massdev_score
Definition: OpenSwathScoring.h:144
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
static std::vector< std::pair< double, double > > removeOutliersIterative(const std::vector< std::pair< double, double > > &pairs, double rsq_limit, double coverage_limit, bool use_chauvenet, const std::string &method)
This function removes potential outliers in a linear regression dataset.
double dotprod_score_dia
Definition: OpenSwathScoring.h:174
double sonar_rsq
Definition: OpenSwathScoring.h:156
double intensity
Definition: OpenSwathScoring.h:162
int ind_num_transitions
Definition: OpenSwathScoring.h:131
double isotope_correlation
Definition: OpenSwathScoring.h:117
double weighted_mi_score
Definition: OpenSwathScoring.h:168
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
double library_dotprod
Definition: OpenSwathScoring.h:161
void setStrictFlag(bool f)
Set the flag for strict mapping.
Definition: MRMFeatureFinderScoring.h:193
bool use_sonar_scores
Definition: OpenSwathScoring.h:73
double isotope_overlap
Definition: OpenSwathScoring.h:119
std::string ind_apex_intensity
Definition: OpenSwathScoring.h:136
A class that calls the scoring routines.
Definition: OpenSwathScoring.h:475
double xcorr_ms1_coelution_score
Definition: OpenSwathScoring.h:146
void setParameters(const Param ¶m)
Sets the parameters.
double sonar_lag
Definition: OpenSwathScoring.h:158
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all features (including subordinates)....
Definition: FeatureMap.h:274
const Param & getDefaults() const
Non-mutable access to the default parameters.
double sonar_trend
Definition: OpenSwathScoring.h:155
static OpenSwath::SpectrumAccessPtr getSpectrumAccessOpenMSPtr(boost::shared_ptr< OpenMS::PeakMap > exp)
Simple Factory method to get a SpectrumAccess Ptr from an MSExperiment.
bool use_sn_score_
Definition: OpenSwathScoring.h:70
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
std::string ind_log_sn_score
Definition: OpenSwathScoring.h:130
static std::pair< double, double > estimateRTRange(const OpenSwath::LightTargetedExperiment &exp)
Estimate the retention time span of a targeted experiment (returns min/max values as a pair)
void addChromatogram(const MSChromatogram &chromatogram)
adds a chromatogram to the list
double weighted_coelution_score
Definition: OpenSwathScoring.h:142
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
std::string ind_mi_ratio
Definition: OpenSwathScoring.h:140
A container for features.
Definition: FeatureMap.h:93
bool use_ms1_correlation
Definition: OpenSwathScoring.h:74
An LC-MS feature.
Definition: Feature.h:70
bool use_ms1_mi
Definition: OpenSwathScoring.h:76
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:89
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
std::string ind_log_intensity
Definition: OpenSwathScoring.h:138
double total_xic
Definition: OpenSwathScoring.h:163
std::string ind_area_intensity
Definition: OpenSwathScoring.h:133
double sn_ratio
Definition: OpenSwathScoring.h:165
double raw_rt_score
Definition: OpenSwathScoring.h:172
A structure to hold the different scores computed by OpenSWATH.
Definition: OpenSwathScoring.h:109
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:270
Management and storage of parameters / INI files.
Definition: Param.h:74
double weighted_xcorr_shape
Definition: OpenSwathScoring.h:143
bool use_intensity_score_
Definition: OpenSwathScoring.h:66
bool use_coelution_score_
Definition: OpenSwathScoring.h:61
double library_manhattan
Definition: OpenSwathScoring.h:160
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
bool use_shape_score_
Definition: OpenSwathScoring.h:62
double xcorr_ms1_shape_score
Definition: OpenSwathScoring.h:147
OpenSwath_Scores()
Definition: OpenSwathScoring.h:177
Definition: TransitionExperiment.h:46
double normalized_experimental_rt
Definition: OpenSwathScoring.h:171
std::string ind_isotope_correlation
Definition: OpenSwathScoring.h:118
std::string ind_total_mi
Definition: OpenSwathScoring.h:137
UInt64 getUniqueId() const
Non-mutable access to unique id - returns the unique id.
Definition: UniqueIdInterface.h:109
bool use_total_mi_score_
Definition: OpenSwathScoring.h:68
double get_quick_lda_score(double library_corr_, double library_norm_manhattan_, double norm_rt_score_, double xcorr_coelution_score_, double xcorr_shape_score_, double log_sn_score_) const
Definition: OpenSwathScoring.h:238
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
void clear(bool clear_meta_data=true)
Clears all data and meta data.
double library_sangle
Definition: OpenSwathScoring.h:115
double ms1_isotope_correlation
Definition: OpenSwathScoring.h:149
bool use_uis_scores
Definition: OpenSwathScoring.h:77
Definition: ITransition.h:55
double ms1_ppm_score
Definition: OpenSwathScoring.h:148
static std::map< std::string, double > simpleFindBestFeature(const OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType &transition_group_map, bool useQualCutoff=false, double qualCutoff=0.0)
Simple method to extract the best Feature for each transition group (e.g. for RT alignment)