35 #ifndef OPENMS_FILTERING_DATAREDUCTION_FEATUREFINDINGMETABO_H
36 #define OPENMS_FILTERING_DATAREDUCTION_FEATUREFINDINGMETABO_H
96 return iso_pattern_.size();
103 if (iso_pattern_.size() > 0)
105 label = iso_pattern_[0]->getLabel();
108 for (
Size i = 1; i < iso_pattern_.size(); ++i)
110 String tmp_str =
"_" + iso_pattern_[i]->getLabel();
119 std::vector<String> tmp_labels;
121 for (
Size i = 0; i < iso_pattern_.size(); ++i)
123 tmp_labels.push_back(iso_pattern_[i]->getLabel());
151 std::vector<double> tmp;
153 for (
Size i = 0; i < iso_pattern_.size(); ++i)
155 tmp.push_back(iso_pattern_[i]->getIntensity(smoothed));
163 if (iso_pattern_.empty())
165 throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__,
"FeatureHypothesis is empty, no centroid MZ!",
String(iso_pattern_.size()));
168 return iso_pattern_[0]->getCentroidMZ();
173 if (iso_pattern_.empty())
175 throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__,
"FeatureHypothesis is empty, no centroid RT!",
String(iso_pattern_.size()));
177 return iso_pattern_[0]->getCentroidRT();
182 if (iso_pattern_.empty())
186 return iso_pattern_[0]->getFWHM();
191 double getMonoisotopicFeatureIntensity(
bool)
const;
192 double getSummedFeatureIntensity(
bool)
const;
194 Size getNumFeatPoints()
const;
195 std::vector<ConvexHull2D> getConvexHulls()
const;
233 void run(std::vector<MassTrace> &,
FeatureMap &);
237 virtual void updateMembers_();
242 double computeOLSCoeff_(
const std::vector<double> &,
const std::vector<double> &);
243 double computeCosineSim_(
const std::vector<double> &,
const std::vector<double> &);
252 void loadIsotopeModel_(
const String&);
260 double computeAveragineSimScore_(
const std::vector<double> &,
const double &);
264 void findLocalFeatures_(std::vector<MassTrace *> &, std::vector<FeatureHypothesis> &);
289 #endif // OPENMS_FILTERING_DATAREDUCTION_FEATUREFINDINGMETABO_H
A more convenient string class.
Definition: String.h:57
Definition: FeatureFindingMetabo.h:207
double getFWHM() const
Definition: FeatureFindingMetabo.h:180
A container for features.
Definition: FeatureMap.h:93
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:128
bool operator()(FeatureHypothesis x, FeatureHypothesis y) const
Definition: FeatureFindingMetabo.h:211
double getScore() const
Definition: FeatureFindingMetabo.h:129
SignedSize getCharge() const
Definition: FeatureFindingMetabo.h:139
Definition: FeatureFindingMetabo.h:77
double getCentroidMZ() const
Returns the centroid m/z.
Definition: MassTrace.h:158
void setCharge(const SignedSize &ch)
Definition: FeatureFindingMetabo.h:144
double getCentroidRT() const
Definition: FeatureFindingMetabo.h:171
std::vector< String > getLabels() const
Definition: FeatureFindingMetabo.h:117
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:65
std::vector< const MassTrace * > iso_pattern_
Definition: FeatureFindingMetabo.h:199
void setScore(const double &score)
Definition: FeatureFindingMetabo.h:134
String getLabel() const
Definition: FeatureFindingMetabo.h:99
SignedSize charge_
Definition: FeatureFindingMetabo.h:202
Invalid value exception.
Definition: Exception.h:336
double feat_score_
Definition: FeatureFindingMetabo.h:200
bool operator()(MassTrace x, MassTrace y) const
Definition: FeatureFindingMetabo.h:69
double getCentroidMZ() const
Definition: FeatureFindingMetabo.h:161
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
Size getSize() const
Definition: FeatureFindingMetabo.h:94
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
std::vector< double > getAllIntensities(bool smoothed=false) const
Definition: FeatureFindingMetabo.h:149
A container type that gathers peaks similar in m/z and moving along retention time.
Definition: MassTrace.h:59