OpenMS  2.4.0
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 
42 
43 #include <vector>
44 #include <svm.h>
45 
46 namespace OpenMS
47 {
48 
57  class OPENMS_DLLAPI FeatureHypothesis
58  {
59 public:
62 
65 
68 
70  FeatureHypothesis& operator=(const FeatureHypothesis& rhs);
71 
72  // getter & setter
73  Size getSize() const;
74 
75  String getLabel() const;
76 
77  std::vector<String> getLabels() const;
78 
79  double getScore() const;
80 
81  void setScore(const double& score);
82 
83  SignedSize getCharge() const;
84 
85  void setCharge(const SignedSize& ch);
86 
87  std::vector<double> getAllIntensities(bool smoothed = false) const;
88 
89  std::vector<double> getAllCentroidMZ() const;
90 
91  std::vector<double> getAllCentroidRT() const;
92 
93  std::vector<double> getIsotopeDistances() const;
94 
95  double getCentroidMZ() const;
96 
97  double getCentroidRT() const;
98 
99  double getFWHM() const;
100 
102  void addMassTrace(const MassTrace&);
103  double getMonoisotopicFeatureIntensity(bool) const;
104  double getSummedFeatureIntensity(bool) const;
105 
106  Size getNumFeatPoints() const;
107  std::vector<ConvexHull2D> getConvexHulls() const;
108  std::vector< OpenMS::MSChromatogram > getChromatograms(UInt64 feature_id) const;
109 
110 private:
111 
112  // pointers of MassTraces contained in isotopic pattern
113  std::vector<const MassTrace*> iso_pattern_;
114 
115  double feat_score_;
116 
118  };
119 
120  class OPENMS_DLLAPI CmpMassTraceByMZ
121  {
122 public:
123 
124  bool operator()(const MassTrace& x, const MassTrace& y) const
125  {
126  return x.getCentroidMZ() < y.getCentroidMZ();
127  }
128 
129  };
130 
131  class OPENMS_DLLAPI CmpHypothesesByScore
132  {
133 public:
134 
135  bool operator()(const FeatureHypothesis& x, const FeatureHypothesis& y) const
136  {
137  return x.getScore() > y.getScore();
138  }
139 
140  };
141 
167  class OPENMS_DLLAPI FeatureFindingMetabo :
168  public DefaultParamHandler,
169  public ProgressLogger
170  {
171 public:
174 
176  ~FeatureFindingMetabo() override;
177 
179  void run(std::vector<MassTrace>& input_mtraces, FeatureMap& output_featmap, std::vector<std::vector< OpenMS::MSChromatogram > >& output_chromatograms);
180 
181 protected:
182  void updateMembers_() override;
183 
184 private:
193  double computeCosineSim_(const std::vector<double>&, const std::vector<double>&) const;
194 
197  double computeOLSCoeff_(const std::vector<double>&, const std::vector<double>&) const;
198 
211  int isLegalIsotopePattern_(const FeatureHypothesis& feat_hypo) const;
212 
213  void loadIsotopeModel_(const String&);
214 
235  double scoreMZ_(const MassTrace &, const MassTrace &, Size isotopic_position, Size charge) const;
236 
249  double scoreRT_(const MassTrace&, const MassTrace&) const;
250 
257  double computeAveragineSimScore_(const std::vector<double>& intensities, const double& molecular_weight) const;
258 
267  void findLocalFeatures_(const std::vector<const MassTrace*>& candidates, const double total_intensity, std::vector<FeatureHypothesis>& output_hypotheses) const;
268 
270  svm_model* isotope_filt_svm_;
271  std::vector<double> svm_feat_centers_;
272  std::vector<double> svm_feat_scales_;
273 
275 
281  double chrom_fwhm_;
282 
287 
291 
293  };
294 
295 }
296 
DefaultParamHandler.h
OpenMS::UniqueIdInterface::ensureUniqueId
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
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:150
OpenMS::Param::copy
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::UInt64
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
OpenMS::FeatureFindingMetabo::charge_lower_bound_
Size charge_lower_bound_
Definition: FeatureFindingMetabo.h:279
OpenMS::FeatureFindingMetabo::enable_RT_filtering_
bool enable_RT_filtering_
Definition: FeatureFindingMetabo.h:284
OpenMS::FeatureFindingMetabo::report_chromatograms_
bool report_chromatograms_
Definition: FeatureFindingMetabo.h:290
OpenMS::FeatureFindingMetabo::chrom_fwhm_
double chrom_fwhm_
Definition: FeatureFindingMetabo.h:281
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:57
OpenMS::FeatureFindingMetabo::local_rt_range_
double local_rt_range_
parameter stuff
Definition: FeatureFindingMetabo.h:277
MzMLFile.h
OpenMS::MassTrace
A container type that gathers peaks similar in m/z and moving along retention time.
Definition: MassTrace.h:61
Feature.h
OpenMS::FeatureFindingMetabo
Method for the assembly of mass traces belonging to the same isotope pattern, i.e....
Definition: FeatureFindingMetabo.h:167
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::PeakFileOptions::addMSLevel
void addMSLevel(int level)
adds a desired MS level for peaks to load
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
FeatureXMLFile.h
OpenMS::FeatureFindingMetabo::use_mz_scoring_C13_
bool use_mz_scoring_C13_
Definition: FeatureFindingMetabo.h:288
OpenMS::FeatureHypothesis::charge_
SignedSize charge_
Definition: FeatureFindingMetabo.h:117
OpenMS::FeatureMap::setPrimaryMSRunPath
void setPrimaryMSRunPath(const StringList &s)
set the file path to the primary MS run (usually the mzML file obtained after data conversion from ra...
OpenMS::CmpHypothesesByScore::operator()
bool operator()(const FeatureHypothesis &x, const FeatureHypothesis &y) const
Definition: FeatureFindingMetabo.h:135
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:127
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::FeatureFindingMetabo::isotope_filtering_model_
String isotope_filtering_model_
Definition: FeatureFindingMetabo.h:285
MassTrace.h
OpenMS::FeatureFindingMetabo::svm_feat_centers_
std::vector< double > svm_feat_centers_
Definition: FeatureFindingMetabo.h:271
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::FeatureFinderAlgorithmSH
The Superhirn FeatureFinderAlgorithm.
Definition: FeatureFinderAlgorithmSH.h:99
OpenMS::FeatureFindingMetabo::isotope_filt_svm_
svm_model * isotope_filt_svm_
SVM parameters.
Definition: FeatureFindingMetabo.h:270
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
LOG_WARN
#define LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:450
ProgressLogger.h
OpenMS::MzMLFile::load
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...
OpenMS::FeatureHypothesis::feat_score_
double feat_score_
Definition: FeatureFindingMetabo.h:115
FeatureMap.h
OpenMS::FeatureFindingMetabo::local_mz_range_
double local_mz_range_
Definition: FeatureFindingMetabo.h:278
OpenMS::DataProcessing::PEAK_PICKING
Peak picking (conversion from raw to peak data)
Definition: DataProcessing.h:67
OpenMS::FeatureFinder
The main feature finder class.
Definition: FeatureFinder.h:56
OpenMS::FeatureFindingMetabo::total_intensity_
double total_intensity_
Definition: FeatureFindingMetabo.h:274
OpenMS::CmpMassTraceByMZ
Definition: FeatureFindingMetabo.h:120
OpenMS::MSExperiment::empty
bool empty() const
Definition: MSExperiment.h:137
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
OpenMS::FeatureXMLFile::store
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
OpenMS::CmpMassTraceByMZ::operator()
bool operator()(const MassTrace &x, const MassTrace &y) const
Definition: FeatureFindingMetabo.h:124
OpenMS::FeatureHypothesis::iso_pattern_
std::vector< const MassTrace * > iso_pattern_
Definition: FeatureFindingMetabo.h:113
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
MSExperiment.h
OpenMS::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:93
OpenMS::FeatureHypothesis
Internal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope gro...
Definition: FeatureFindingMetabo.h:57
MSChromatogram.h
OpenMS::FeatureFindingMetabo::remove_single_traces_
bool remove_single_traces_
Definition: FeatureFindingMetabo.h:292
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
OpenMS::MSExperiment::getPrimaryMSRunPath
void getPrimaryMSRunPath(StringList &toFill) const
get the file path to the first MS run
OpenMS::DataProcessing::QUANTITATION
Quantitation.
Definition: DataProcessing.h:72
FeatureFinderAlgorithmSH.h
OpenMS::FeatureFindingMetabo::charge_upper_bound_
Size charge_upper_bound_
Definition: FeatureFindingMetabo.h:280
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:74
OpenMS::FeatureFindingMetabo::svm_feat_scales_
std::vector< double > svm_feat_scales_
Definition: FeatureFindingMetabo.h:272
OpenMS::CmpHypothesesByScore
Definition: FeatureFindingMetabo.h:131
OpenMS::FeatureFindingMetabo::use_smoothed_intensities_
bool use_smoothed_intensities_
Definition: FeatureFindingMetabo.h:286
OpenMS::MassTrace::getCentroidMZ
double getCentroidMZ() const
Returns the centroid m/z.
Definition: MassTrace.h:178
OpenMS::FeatureFindingMetabo::report_convex_hulls_
bool report_convex_hulls_
Definition: FeatureFindingMetabo.h:289
OpenMS::MzMLFile::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h
OpenMS::FeatureHypothesis::getScore
double getScore() const
OpenMS::FeatureFindingMetabo::report_summed_ints_
bool report_summed_ints_
Definition: FeatureFindingMetabo.h:283