OpenMS  2.5.0
FeatureFindingMetabo.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Erhan Kenar, Holger Franken $
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34 
35 #pragma once
36 
43 
44 #include <vector>
45 #include <svm.h>
46 
47 namespace OpenMS
48 {
49 
58  class OPENMS_DLLAPI FeatureHypothesis
59  {
60 public:
63 
66 
69 
71  FeatureHypothesis& operator=(const FeatureHypothesis& rhs);
72 
73  // getter & setter
74  Size getSize() const;
75 
76  String getLabel() const;
77 
78  std::vector<String> getLabels() const;
79 
80  double getScore() const;
81 
82  void setScore(const double& score);
83 
84  SignedSize getCharge() const;
85 
86  void setCharge(const SignedSize& ch);
87 
88  std::vector<double> getAllIntensities(bool smoothed = false) const;
89 
90  std::vector<double> getAllCentroidMZ() const;
91 
92  std::vector<double> getAllCentroidRT() const;
93 
94  std::vector<double> getIsotopeDistances() const;
95 
96  double getCentroidMZ() const;
97 
98  double getCentroidRT() const;
99 
100  double getFWHM() const;
101 
103  void addMassTrace(const MassTrace&);
104  double getMonoisotopicFeatureIntensity(bool) const;
105  double getSummedFeatureIntensity(bool) const;
106 
107  Size getNumFeatPoints() const;
108  std::vector<ConvexHull2D> getConvexHulls() const;
109  std::vector< OpenMS::MSChromatogram > getChromatograms(UInt64 feature_id) const;
110 
111 private:
112 
113  // pointers of MassTraces contained in isotopic pattern
114  std::vector<const MassTrace*> iso_pattern_;
115 
116  double feat_score_;
117 
119  };
120 
121  class OPENMS_DLLAPI CmpMassTraceByMZ
122  {
123 public:
124 
125  bool operator()(const MassTrace& x, const MassTrace& y) const
126  {
127  return x.getCentroidMZ() < y.getCentroidMZ();
128  }
129 
130  };
131 
132  class OPENMS_DLLAPI CmpHypothesesByScore
133  {
134 public:
135 
136  bool operator()(const FeatureHypothesis& x, const FeatureHypothesis& y) const
137  {
138  return x.getScore() > y.getScore();
139  }
140 
141  };
142 
146  struct OPENMS_DLLAPI Range
147 {
150 };
151 
177  class OPENMS_DLLAPI FeatureFindingMetabo :
178  public DefaultParamHandler,
179  public ProgressLogger
180  {
181 public:
184 
186  ~FeatureFindingMetabo() override;
187 
189  void run(std::vector<MassTrace>& input_mtraces, FeatureMap& output_featmap, std::vector<std::vector< OpenMS::MSChromatogram > >& output_chromatograms);
190 
191 protected:
192  void updateMembers_() override;
193 
194 private:
200  std::vector<const Element*> elementsFromString_(const std::string& elements_string) const;
208  Range getTheoreticIsotopicMassWindow_(const std::vector<Element const *> alphabet, int peakOffset) const;
209 
218  double computeCosineSim_(const std::vector<double>&, const std::vector<double>&) const;
219 
232  int isLegalIsotopePattern_(const FeatureHypothesis& feat_hypo) const;
233 
234  void loadIsotopeModel_(const String&);
235 
259  double scoreMZ_(const MassTrace &, const MassTrace &, Size isotopic_position, Size charge, Range isotope_window) const;
260 
269  double scoreMZByExpectedMean_(Size iso_pos, Size charge, const double diff_mz, double mt_variances) const;
270 
279  double scoreMZByExpectedRange_(Size charge, const double diff_mz, double mt_variances, Range isotope_window) const;
280 
293  double scoreRT_(const MassTrace&, const MassTrace&) const;
294 
301  double computeAveragineSimScore_(const std::vector<double>& intensities, const double& molecular_weight) const;
302 
311  void findLocalFeatures_(const std::vector<const MassTrace*>& candidates, double total_intensity, std::vector<FeatureHypothesis>& output_hypotheses) const;
312 
314  svm_model* isotope_filt_svm_;
315  std::vector<double> svm_feat_centers_;
316  std::vector<double> svm_feat_scales_;
317 
319 
325  double chrom_fwhm_;
326 
331 
336 
338  std::vector<const Element*> elements_;
339  };
340 
341 }
342 
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