OpenMS  2.8.0
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 
46 struct svm_model;
47 
48 namespace OpenMS
49 {
50 
59  class OPENMS_DLLAPI FeatureHypothesis
60  {
61 public:
63  FeatureHypothesis() = default;
64 
66  ~FeatureHypothesis() = default;
67 
70 
73 
74  // getter & setter
75  Size getSize() const;
76 
77  String getLabel() const;
78 
79  std::vector<String> getLabels() const;
80 
81  double getScore() const;
82 
83  void setScore(const double& score);
84 
86 
87  void setCharge(const SignedSize& ch);
88 
89  std::vector<double> getAllIntensities(bool smoothed = false) const;
90 
91  std::vector<double> getAllCentroidMZ() const;
92 
93  std::vector<double> getAllCentroidRT() const;
94 
95  std::vector<double> getIsotopeDistances() const;
96 
97  double getCentroidMZ() const;
98 
99  double getCentroidRT() const;
100 
101  double getFWHM() const;
102 
104  void addMassTrace(const MassTrace&);
106  double getSummedFeatureIntensity(bool) const;
107 
109  double getMaxIntensity(bool smoothed = false) const;
110 
112  std::vector<ConvexHull2D> getConvexHulls() const;
113  std::vector< OpenMS::MSChromatogram > getChromatograms(UInt64 feature_id) const;
114 
115 private:
116 
117  // pointers of MassTraces contained in isotopic pattern
118  std::vector<const MassTrace*> iso_pattern_;
119 
120  double feat_score_{};
121 
122  SignedSize charge_{};
123  };
124 
125  class OPENMS_DLLAPI CmpMassTraceByMZ
126  {
127 public:
128 
129  bool operator()(const MassTrace& x, const MassTrace& y) const
130  {
131  return x.getCentroidMZ() < y.getCentroidMZ();
132  }
133 
134  };
135 
136  class OPENMS_DLLAPI CmpHypothesesByScore
137  {
138 public:
139 
140  bool operator()(const FeatureHypothesis& x, const FeatureHypothesis& y) const
141  {
142  return x.getScore() > y.getScore();
143  }
144 
145  };
146 
150  struct OPENMS_DLLAPI Range
151 {
154 };
155 
181  class OPENMS_DLLAPI FeatureFindingMetabo :
182  public DefaultParamHandler,
183  public ProgressLogger
184  {
185 public:
188 
191 
193  void run(std::vector<MassTrace>& input_mtraces, FeatureMap& output_featmap, std::vector<std::vector< OpenMS::MSChromatogram > >& output_chromatograms);
194 
195 protected:
196  void updateMembers_() override;
197 
198 private:
204  std::vector<const Element*> elementsFromString_(const std::string& elements_string) const;
212  Range getTheoreticIsotopicMassWindow_(const std::vector<Element const *> alphabet, int peakOffset) const;
213 
222  double computeCosineSim_(const std::vector<double>&, const std::vector<double>&) const;
223 
236  int isLegalIsotopePattern_(const FeatureHypothesis& feat_hypo) const;
237 
238  void loadIsotopeModel_(const String&);
239 
263  double scoreMZ_(const MassTrace &, const MassTrace &, Size isotopic_position, Size charge, Range isotope_window) const;
264 
273  double scoreMZByExpectedMean_(Size iso_pos, Size charge, const double diff_mz, double mt_variances) const;
274 
283  double scoreMZByExpectedRange_(Size charge, const double diff_mz, double mt_variances, Range isotope_window) const;
284 
296  double scoreRT_(const MassTrace&, const MassTrace&) const;
297 
304  double computeAveragineSimScore_(const std::vector<double>& intensities, const double& molecular_weight) const;
305 
314  void findLocalFeatures_(const std::vector<const MassTrace*>& candidates, double total_intensity, std::vector<FeatureHypothesis>& output_hypotheses) const;
315 
317  svm_model* isotope_filt_svm_ = nullptr;
318  std::vector<double> svm_feat_centers_;
319  std::vector<double> svm_feat_scales_;
320 
321  //unused
322  //double total_intensity_;
323 
329  double chrom_fwhm_;
330 
335 
340 
342  std::vector<const Element*> elements_;
343  };
344 
345 }
346 
Definition: FeatureFindingMetabo.h:137
bool operator()(const FeatureHypothesis &x, const FeatureHypothesis &y) const
Definition: FeatureFindingMetabo.h:140
Definition: FeatureFindingMetabo.h:126
bool operator()(const MassTrace &x, const MassTrace &y) const
Definition: FeatureFindingMetabo.h:129
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:93
Method for the assembly of mass traces belonging to the same isotope pattern, i.e....
Definition: FeatureFindingMetabo.h:184
void findLocalFeatures_(const std::vector< const MassTrace * > &candidates, double total_intensity, std::vector< FeatureHypothesis > &output_hypotheses) const
Identify groupings of mass traces based on a set of reasonable candidates.
FeatureFindingMetabo()
Default constructor.
String isotope_filtering_model_
Definition: FeatureFindingMetabo.h:333
std::vector< const Element * > elementsFromString_(const std::string &elements_string) const
parses a string of element symbols into a vector of Elements
Size charge_upper_bound_
Definition: FeatureFindingMetabo.h:328
~FeatureFindingMetabo() override
Default destructor.
bool use_mz_scoring_C13_
Definition: FeatureFindingMetabo.h:336
bool report_chromatograms_
Definition: FeatureFindingMetabo.h:339
std::vector< double > svm_feat_centers_
Definition: FeatureFindingMetabo.h:318
double scoreMZ_(const MassTrace &, const MassTrace &, Size isotopic_position, Size charge, Range isotope_window) const
Perform mass to charge scoring of two multiple mass traces.
bool report_summed_ints_
Definition: FeatureFindingMetabo.h:331
bool report_convex_hulls_
Definition: FeatureFindingMetabo.h:338
Size charge_lower_bound_
Definition: FeatureFindingMetabo.h:327
double computeCosineSim_(const std::vector< double > &, const std::vector< double > &) const
Computes the cosine similarity between two vectors.
std::vector< double > svm_feat_scales_
Definition: FeatureFindingMetabo.h:319
double scoreMZByExpectedRange_(Size charge, const double diff_mz, double mt_variances, Range isotope_window) const
score isotope m/z distance based on an expected isotope window which was calculated from a set of exp...
void run(std::vector< MassTrace > &input_mtraces, FeatureMap &output_featmap, std::vector< std::vector< OpenMS::MSChromatogram > > &output_chromatograms)
main method of FeatureFindingMetabo
double local_rt_range_
parameter stuff
Definition: FeatureFindingMetabo.h:325
bool use_mz_scoring_by_element_range_
Definition: FeatureFindingMetabo.h:337
double local_mz_range_
Definition: FeatureFindingMetabo.h:326
double scoreMZByExpectedMean_(Size iso_pos, Size charge, const double diff_mz, double mt_variances) const
score isotope m/z distance based on the expected m/z distances using C13-C12 or Kenar method
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
double scoreRT_(const MassTrace &, const MassTrace &) const
Perform retention time scoring of two multiple mass traces.
std::vector< const Element * > elements_
Definition: FeatureFindingMetabo.h:342
int isLegalIsotopePattern_(const FeatureHypothesis &feat_hypo) const
Compare intensities of feature hypothesis with model.
bool remove_single_traces_
Definition: FeatureFindingMetabo.h:341
double chrom_fwhm_
Definition: FeatureFindingMetabo.h:329
void loadIsotopeModel_(const String &)
bool enable_RT_filtering_
Definition: FeatureFindingMetabo.h:332
double computeAveragineSimScore_(const std::vector< double > &intensities, const double &molecular_weight) const
Perform intensity scoring using the averagine model (for peptides only)
bool use_smoothed_intensities_
Definition: FeatureFindingMetabo.h:334
Range getTheoreticIsotopicMassWindow_(const std::vector< Element const * > alphabet, int peakOffset) const
Internal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope gro...
Definition: FeatureFindingMetabo.h:60
std::vector< String > getLabels() const
double getCentroidMZ() const
FeatureHypothesis()=default
default constructor
void addMassTrace(const MassTrace &)
addMassTrace
void setCharge(const SignedSize &ch)
FeatureHypothesis(const FeatureHypothesis &)=default
copy constructor
std::vector< double > getAllCentroidRT() const
FeatureHypothesis & operator=(const FeatureHypothesis &rhs)=default
assignment operator
std::vector< OpenMS::MSChromatogram > getChromatograms(UInt64 feature_id) const
std::vector< double > getAllIntensities(bool smoothed=false) const
void setScore(const double &score)
std::vector< double > getAllCentroidMZ() const
std::vector< ConvexHull2D > getConvexHulls() const
double getMonoisotopicFeatureIntensity(bool) const
std::vector< const MassTrace * > iso_pattern_
Definition: FeatureFindingMetabo.h:118
double getSummedFeatureIntensity(bool) const
std::vector< double > getIsotopeDistances() const
double getCentroidRT() const
~FeatureHypothesis()=default
default destructor
Size getNumFeatPoints() const
SignedSize getCharge() const
double getMaxIntensity(bool smoothed=false) const
return highest apex of all isotope traces
A container for features.
Definition: FeatureMap.h:106
A container type that gathers peaks similar in m/z and moving along retention time.
Definition: MassTrace.h:62
double getCentroidMZ() const
Returns the centroid m/z.
Definition: MassTrace.h:179
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
A more convenient string class.
Definition: String.h:60
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
double left_boundary
Definition: FeatureFindingMetabo.h:152
double right_boundary
Definition: FeatureFindingMetabo.h:153
Internal structure to store a lower and upper bound of an m/z range.
Definition: FeatureFindingMetabo.h:151