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