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OpenMS
2.5.0
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80 float operator()(
const std::pair<float, float> & a,
const std::pair<float, float> & b)
const;
88 float operator()(
const std::pair<float, float> &
c)
const;
98 void setScale(
float x);
Management and storage of parameters / INI files.
Definition: Param.h:73
Resolves shared peptides based on protein scores.
Definition: PeptideProteinResolution.h:86
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
static void removeUnreferencedProteins(std::vector< ProteinIdentification > &proteins, const std::vector< PeptideIdentification > &peptides)
Removes protein hits from proteins that are not referenced by a peptide in peptides.
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
static bool updateProteinGroups(std::vector< ProteinIdentification::ProteinGroup > &groups, const std::vector< ProteinHit > &hits)
Update protein groups after protein hits were filtered.
void updateRanges() override
Updates minimum and maximum position/intensity.
const Param & getParameters() const
Non-mutable access to the parameters.
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
ExitCodes
Exit codes.
Definition: TOPPBase.h:149
void setPrimaryMSRunPath(const StringList &s)
set the file paths to the primary MS run (stored in ColumnHeaders)
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:121
void setMZ(CoordinateType coordinate)
Mutable access to the m/z coordinate (index 1)
Definition: Peak2D.h:202
Implements the isotope wavelet feature finder.
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:59
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
CoordinateType getMZ() const
Returns the m/z coordinate (index 1)
Definition: Peak2D.h:196
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:104
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:347
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:112
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
A container for features.
Definition: FeatureMap.h:95
Param getSubsectionDefaults_(const String &) const override
This method should return the default parameters for subsections.
Definition: Epifany.cpp:162
Iterator begin()
Definition: MSExperiment.h:157
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
Epifany()
Definition: Epifany.cpp:112
Base class for TOPP applications.
Definition: TOPPBase.h:144
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
int main(int argc, const char **argv)
Definition: Epifany.cpp:364
An LC-MS feature.
Definition: Feature.h:70
CompareFunctor for 2Dpoints.
Definition: EuclideanSimilarity.h:51
Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimenta...
Definition: BayesianProteinInferenceAlgorithm.h:75
Iterator end()
Definition: MSExperiment.h:167
std::vector< String > accessions
Accessions of (indistinguishable) proteins that belong to the same group.
Definition: ProteinIdentification.h:98
void setPrimaryMSRunPath(const StringList &s)
set the file path to the primary MS run (usually the mzML file obtained after data conversion from ra...
void run(const String &algorithm_name, PeakMap &input_map, FeatureMap &features, const Param ¶m, const FeatureMap &seeds)
Executes the FeatureFinder using the given algorithm.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
void insert(const ConsensusFeature &cf)
Adds all feature handles (of the CF) into the consensus feature.
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
void applyBasic(std::vector< PeptideIdentification > &ids)
simpler reimplemetation of the apply function above.
const double NEUTRON_MASS_U
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
A container for consensus elements.
Definition: ConsensusMap.h:79
String toString() const
get a compact representation of the current time status.
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
void registerOptionsAndFlags_() override
Sets the valid command line options (with argument) and flags (without argument).
Definition: Epifany.cpp:119
void setParameters(const Param ¶m)
Sets the parameters.
The main feature finder class.
Definition: FeatureFinder.h:56
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
Bundles multiple (e.g. indistinguishable) proteins in a group.
Definition: ProteinIdentification.h:81
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
No progress logging.
Definition: ProgressLogger.h:74
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
void inferPosteriorProbabilities(std::vector< ProteinIdentification > &proteinIDs, std::vector< PeptideIdentification > &peptideIDs, boost::optional< const ExperimentalDesign > exp_des=boost::optional< const ExperimentalDesign >())
IntensityType getIntensity() const
Definition: Peak2D.h:166
void resolveGraph(ProteinIdentification &protein, std::vector< PeptideIdentification > &peptides)
float scale_
Definition: EuclideanSimilarity.h:55
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...
Used to load and store idXML files.
Definition: IdXMLFile.h:63
File adapter for MzML files.
Definition: MzMLFile.h:55
void convertPSMScores_(vector< PeptideIdentification > &mergedpeps)
Definition: Epifany.cpp:190
static double absdev(IteratorType begin, IteratorType end, double mean=std::numeric_limits< double >::max())
Calculates the absolute deviation of a range of values.
Definition: StatisticFunctions.h:320
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
String & toLower()
Converts the string to lowercase.
ExitCodes main(int argc, const char **argv)
Main routine of all TOPP applications.
A more convenient string class.
Definition: String.h:58
void store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
pair< double, double > checkExtremePSMScores_(vector< PeptideIdentification > &mergedpeps)
Definition: Epifany.cpp:167
Creates a new Protein ID run into which other runs can be inserted. Creates union of protein hits but...
Definition: IDMergerAlgorithm.h:61
void removeExtremeValues_(vector< PeptideIdentification > &mergedpeps, double minscore, double maxscore)
Definition: Epifany.cpp:222
Calculates false discovery rates (FDR) from identifications.
Definition: FalseDiscoveryRate.h:77
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
void buildGraph(ProteinIdentification &protein, const std::vector< PeptideIdentification > &peptides, bool skip_sort=false)
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
StopWatch Class.
Definition: StopWatch.h:59
Definition: Epifany.cpp:108
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
void setRT(double rt)
Sets the absolute retention time (in seconds)
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
ExitCodes main_(int, const char **) override
The actual "main" method. main_() is invoked by main().
Definition: Epifany.cpp:235