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<DoubleReal> 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()));
180 return iso_pattern_[0]->getCentroidRT();
185 if (iso_pattern_.empty())
190 return iso_pattern_[0]->estimateFWHM(use_smoothed_ints);
195 DoubleReal getMonoisotopicFeatureIntensity(
bool);
199 Size getNumFeatPoints()
const;
200 std::vector<ConvexHull2D> getConvexHulls()
const;
242 virtual void updateMembers_();
247 DoubleReal computeOLSCoeff_(
const std::vector<DoubleReal> &,
const std::vector<DoubleReal> &);
248 DoubleReal computeCosineSim_(
const std::vector<DoubleReal> &,
const std::vector<DoubleReal> &);
257 void loadIsotopeModel_(
const String&);
269 void findLocalFeatures_(std::vector<MassTrace *> &, std::vector<FeatureHypothesis> &);
294 #endif // OPENMS_FILTERING_DATAREDUCTION_FEATUREFINDINGMETABO_H
DoubleReal getFWHM(bool use_smoothed_ints=false)
Definition: FeatureFindingMetabo.h:183
A more convenient string class.
Definition: String.h:56
Definition: FeatureFindingMetabo.h:212
DoubleReal getCentroidRT()
Definition: FeatureFindingMetabo.h:171
DoubleReal feat_score_
Definition: FeatureFindingMetabo.h:205
DoubleReal getScore()
Definition: FeatureFindingMetabo.h:129
std::vector< MassTrace * > iso_pattern_
Definition: FeatureFindingMetabo.h:204
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:151
bool operator()(FeatureHypothesis x, FeatureHypothesis y) const
Definition: FeatureFindingMetabo.h:216
Definition: FeatureFindingMetabo.h:77
void setScore(const DoubleReal &score)
Definition: FeatureFindingMetabo.h:134
String getLabel()
Definition: FeatureFindingMetabo.h:99
std::vector< DoubleReal > getAllIntensities(bool smoothed=false)
Definition: FeatureFindingMetabo.h:149
SignedSize getCharge()
Definition: FeatureFindingMetabo.h:139
void setCharge(const SignedSize &ch)
Definition: FeatureFindingMetabo.h:144
DoubleReal getCentroidMZ()
Definition: FeatureFindingMetabo.h:161
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
SignedSize charge_
Definition: FeatureFindingMetabo.h:207
Invalid value exception.
Definition: Exception.h:336
DoubleReal getCentroidMZ()
Returns the centroid m/z.
Definition: MassTrace.h:157
bool operator()(MassTrace x, MassTrace y) const
Definition: FeatureFindingMetabo.h:69
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
Base class for all classes that want to report their progess.
Definition: ProgressLogger.h:56
Size getSize() const
Definition: FeatureFindingMetabo.h:94
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:90
A container type that gathers peaks similar in m/z and moving along retention time.
Definition: MassTrace.h:59
std::vector< String > getLabels()
Definition: FeatureFindingMetabo.h:117