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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);
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.
Resolves shared peptides based on protein scores.
Definition: PeptideProteinResolution.h:86
Implements the isotope wavelet feature finder.
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:59
Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimenta...
Definition: BayesianProteinInferenceAlgorithm.h:75
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
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.
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:121
float scale_
Definition: EuclideanSimilarity.h:55
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:58
std::vector< String > accessions
Accessions of (indistinguishable) proteins that belong to the same group.
Definition: ProteinIdentification.h:98
Iterator begin()
Definition: MSExperiment.h:157
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
static bool updateProteinGroups(std::vector< ProteinIdentification::ProteinGroup > &groups, const std::vector< ProteinHit > &hits)
Update protein groups after protein hits were filtered.
IntensityType getIntensity() const
Definition: Peak2D.h:166
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:112
void setPrimaryMSRunPath(const StringList &s)
set the file path to the primary MS run (usually the mzML file obtained after data conversion from ra...
Creates a new Protein ID run into which other runs can be inserted. Creates union of protein hits but...
Definition: IDMergerAlgorithm.h:61
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
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.
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
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...
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
The main feature finder class.
Definition: FeatureFinder.h:56
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
void setMZ(CoordinateType coordinate)
Mutable access to the m/z coordinate (index 1)
Definition: Peak2D.h:202
void setParameters(const Param ¶m)
Sets the parameters.
const Param & getParameters() const
Non-mutable access to the parameters.
void resolveGraph(ProteinIdentification &protein, std::vector< PeptideIdentification > &peptides)
String toString() const
get a compact representation of the current time status.
CompareFunctor for 2Dpoints.
Definition: EuclideanSimilarity.h:51
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
A container for consensus elements.
Definition: ConsensusMap.h:79
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.
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
StopWatch Class.
Definition: StopWatch.h:59
Calculates false discovery rates (FDR) from identifications.
Definition: FalseDiscoveryRate.h:77
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
void buildGraph(ProteinIdentification &protein, const std::vector< PeptideIdentification > &peptides, bool skip_sort=false)
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
A container for features.
Definition: FeatureMap.h:95
An LC-MS feature.
Definition: Feature.h:70
Iterator end()
Definition: MSExperiment.h:167
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
void updateRanges() override
Updates minimum and maximum position/intensity.
Management and storage of parameters / INI files.
Definition: Param.h:73
void applyBasic(std::vector< PeptideIdentification > &ids)
simpler reimplemetation of the apply function above.
No progress logging.
Definition: ProgressLogger.h:74
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
CoordinateType getMZ() const
Returns the m/z coordinate (index 1)
Definition: Peak2D.h:196
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
const double NEUTRON_MASS_U
void run(const String &algorithm_name, PeakMap &input_map, FeatureMap &features, const Param ¶m, const FeatureMap &seeds)
Executes the FeatureFinder using the given algorithm.
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:104
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
void setRT(double rt)
Sets the absolute retention time (in seconds)
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
void setPrimaryMSRunPath(const StringList &s)
set the file paths to the primary MS run (stored in ColumnHeaders)
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 insert(const ConsensusFeature &cf)
Adds all feature handles (of the CF) into the consensus feature.
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
Used to load and store idXML files.
Definition: IdXMLFile.h:63
String & toLower()
Converts the string to lowercase.
Bundles multiple (e.g. indistinguishable) proteins in a group.
Definition: ProteinIdentification.h:81