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OpenMS
2.6.0
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Go to the documentation of this file.
78 std::vector<String> getLabels()
const;
80 double getScore()
const;
82 void setScore(
const double& score);
88 std::vector<double> getAllIntensities(
bool smoothed =
false)
const;
90 std::vector<double> getAllCentroidMZ()
const;
92 std::vector<double> getAllCentroidRT()
const;
94 std::vector<double> getIsotopeDistances()
const;
96 double getCentroidMZ()
const;
98 double getCentroidRT()
const;
100 double getFWHM()
const;
104 double getMonoisotopicFeatureIntensity(
bool)
const;
105 double getSummedFeatureIntensity(
bool)
const;
107 Size getNumFeatPoints()
const;
108 std::vector<ConvexHull2D> getConvexHulls()
const;
109 std::vector< OpenMS::MSChromatogram > getChromatograms(
UInt64 feature_id)
const;
189 void run(std::vector<MassTrace>& input_mtraces,
FeatureMap& output_featmap, std::vector<std::vector< OpenMS::MSChromatogram > >& output_chromatograms);
192 void updateMembers_()
override;
200 std::vector<const Element*> elementsFromString_(
const std::string& elements_string)
const;
208 Range getTheoreticIsotopicMassWindow_(
const std::vector<Element const *> alphabet,
int peakOffset)
const;
218 double computeCosineSim_(
const std::vector<double>&,
const std::vector<double>&)
const;
234 void loadIsotopeModel_(
const String&);
269 double scoreMZByExpectedMean_(
Size iso_pos,
Size charge,
const double diff_mz,
double mt_variances)
const;
279 double scoreMZByExpectedRange_(
Size charge,
const double diff_mz,
double mt_variances,
Range isotope_window)
const;
301 double computeAveragineSimScore_(
const std::vector<double>& intensities,
const double& molecular_weight)
const;
311 void findLocalFeatures_(
const std::vector<const MassTrace*>& candidates,
double total_intensity, std::vector<FeatureHypothesis>& output_hypotheses)
const;
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:154
Base class for TOPP applications.
Definition: TOPPBase.h:144
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
static String basename(const String &file)
Returns the basename of the file (without the path).
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:59
A container type that gathers peaks similar in m/z and moving along retention time.
Definition: MassTrace.h:61
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
void addMSLevel(int level)
adds a desired MS level for peaks to load
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
SignedSize charge_
Definition: FeatureFindingMetabo.h:118
void setPrimaryMSRunPath(const StringList &s)
set the file path to the primary MS run (usually the mzML file obtained after data conversion from ra...
bool operator()(const FeatureHypothesis &x, const FeatureHypothesis &y) const
Definition: FeatureFindingMetabo.h:136
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
Size size() const
Definition: MSExperiment.h:127
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Internal structure to store a lower and upper bound of an m/z range.
Definition: FeatureFindingMetabo.h:146
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
The Superhirn FeatureFinderAlgorithm.
Definition: FeatureFinderAlgorithmSH.h:99
double right_boundary
Definition: FeatureFindingMetabo.h:149
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
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...
double feat_score_
Definition: FeatureFindingMetabo.h:116
double left_boundary
Definition: FeatureFindingMetabo.h:148
Peak picking (conversion from raw to peak data)
Definition: DataProcessing.h:67
The main feature finder class.
Definition: FeatureFinder.h:56
Definition: FeatureFindingMetabo.h:121
bool empty() const
Definition: MSExperiment.h:137
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
bool operator()(const MassTrace &x, const MassTrace &y) const
Definition: FeatureFindingMetabo.h:125
std::vector< const MassTrace * > iso_pattern_
Definition: FeatureFindingMetabo.h:114
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
A container for features.
Definition: FeatureMap.h:97
Internal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope gro...
Definition: FeatureFindingMetabo.h:58
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
Quantitation.
Definition: DataProcessing.h:72
Management and storage of parameters / INI files.
Definition: Param.h:73
Definition: FeatureFindingMetabo.h:132
double getCentroidMZ() const
Returns the centroid m/z.
Definition: MassTrace.h:179
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!