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OpenMS
2.6.0
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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.
static ExperimentalDesign load(const String &tsv_file, bool require_spectra_files)
Loads an experimental design from a tabular separated file.
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.
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
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:59
std::vector< String > accessions
Accessions of (indistinguishable) proteins that belong to the same group.
Definition: ProteinIdentification.h:134
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
OpenMS consensus map format (.consensusXML)
Definition: FileTypes.h:67
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Representation of a protein hit.
Definition: ProteinHit.h:58
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...
void switchToGeneralScoreType(std::vector< PeptideIdentification > &id, ScoreType type, Size &counter)
Definition: IDScoreSwitcherAlgorithm.h:111
void mergeAllIDRuns(ConsensusMap &cmap) const
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
#define OPENMS_LOG_FATAL_ERROR
Macro to be used if fatal error are reported (processing stops)
Definition: LogStream.h:450
void mergeProteinsAcrossFractionsAndReplicates(ConsensusMap &cmap, const ExperimentalDesign &exp_design) const
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
const String & getAccession() const
returns the accession of the protein
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
static void removeUnreferencedProteins(ConsensusMap &cmap, bool include_unassigned)
Merges identification data in ConsensusMaps.
Definition: ConsensusMapMergerAlgorithm.h:63
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...
void reset()
Clear the stop watch but keep running.
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
Type
Actual file types enum.
Definition: FileTypes.h:58
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
void start()
Start the stop watch.
The main feature finder class.
Definition: FeatureFinder.h:56
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
Definition: IDScoreSwitcherAlgorithm.h:47
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 stop()
Stop the stop watch (can be resumed later). If the stop watch was not running an exception is thrown.
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:80
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
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
This class is used to determine the current process' CPU (user and/or kernel) and wall time.
Definition: StopWatch.h:65
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.
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
A container for features.
Definition: FeatureMap.h:97
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
static Type nameToType(const String &name)
Converts a file type name into a Type.
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:128
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:62
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:117