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OpenMS
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73 void rip(std::map<
String, std::pair<std::vector<ProteinIdentification>, std::vector<PeptideIdentification> > > & ripped, std::vector<ProteinIdentification> & proteins, std::vector<PeptideIdentification> & peptides);
86 void getProteinHits_(std::vector<ProteinHit> & result,
const std::vector<ProteinHit> & protein_hits,
const std::vector<String> & protein_accessions);
88 void getProteinAccessions_(std::vector<String> & result,
const std::vector<PeptideHit> & peptide_hits);
void getSpectrumAlignment(std::vector< std::pair< Size, Size > > &alignment, const SpectrumType1 &s1, const SpectrumType2 &s2) const
Definition: SpectrumAlignment.h:86
Implements a fitter for Gaussian functions.
Definition: GaussFitter.h:58
Int getCharge() const
returns the charge of the peptide
static std::map< String, std::vector< std::vector< double > > > extractAndTransformScores(const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const bool split_charge, const bool top_hits_only, const bool target_decoy_available, const double fdr_for_targets_smaller)
extract and transform score types to a range and score orientation that the PEP model can handle
Base class for TOPP applications.
Definition: TOPPBase.h:150
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
Normalizes the peak intensities spectrum-wise.
Definition: Normalizer.h:57
void setX(CoordinateType c)
Name mutator for the first dimension. Only for DPosition<2>, for visualization.
Definition: DPosition.h:164
const std::vector< ProteinGroup > & getIndistinguishableProteins() const
Returns the indistinguishable proteins.
static double median(IteratorType begin, IteratorType end, bool sorted=false)
Calculates the median of a range of values.
Definition: StatisticFunctions.h:152
double getSignificanceThreshold() const
Returns the protein significance threshold value.
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
static String basename(const String &file)
Returns the basename of the file (without the path).
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
struct of parameters of a Gaussian distribution
Definition: GaussFitter.h:63
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:57
GaussFitResult fit(std::vector< DPosition< 2 > > &points) const
Fits a Gaussian distribution to the given data points.
Precondition failed exception.
Definition: Exception.h:166
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
double getMonoWeight(Residue::ResidueType type=Residue::Full, Int charge=0) const
Representation of a protein hit.
Definition: ProteinHit.h:53
std::vector< ProteinHit >::iterator findHit(const String &accession)
Finds a protein hit by accession (returns past-the-end iterator if not found)
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
String toString() const
returns the peptide as string with modifications embedded in brackets
void filterSpectrum(SpectrumType &spectrum) const
Definition: Normalizer.h:86
virtual void getSpectrum(PeakSpectrum &spec, const AASequence &peptide, Int min_charge, Int max_charge) const
returns a spectrum with the ion types, that are set in the tool parameters
const double PROTON_MASS_U
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
static DateTime now()
Returns the current date and time.
static bool writable(const String &file)
Return true if the file is writable.
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
bool fit(std::vector< double > &search_engine_scores)
fits the distributions to the data points(search_engine_scores). Estimated parameters for the distrib...
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:347
Aligns the peaks of two sorted spectra Method 1: Using a banded (width via 'tolerance' parameter) ali...
Definition: SpectrumAlignment.h:65
Ripping protein/peptide identification according their file origin.
Definition: IDRipper.h:52
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::vector< SpectrumType >::iterator Iterator
Mutable iterator.
Definition: MSExperiment.h:111
#define LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:458
Representation of a histogram.
Definition: Histogram.h:63
#define LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:450
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
bool exists(const String &key) const
Tests if a parameter is set (expecting its fully qualified name, e.g., TextExporter:1:proteins_only)
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...
const std::vector< ProteinHit > & getHits() const
Returns the protein hits.
static void updateScores(const PosteriorErrorProbabilityModel &PEP_model, const String &search_engine, const Int charge, const bool prob_correct, const bool split_charge, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, bool &unable_to_fit_data, bool &data_might_not_be_well_fit)
update score entries with PEP (or 1-PEP) estimates
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
void setParameters(const Param ¶m)
Sets the parameters.
QString toQString() const
Conversion to Qt QString.
void setY(CoordinateType c)
Name mutator for the second dimension. Only for DPosition<2>, for visualization.
Definition: DPosition.h:171
const Param & getParameters() const
Non-mutable access to the parameters.
std::set< String > extractProteinAccessionsSet() const
extracts the set of non-empty protein accessions from peptide evidences
void rip(std::map< String, std::pair< std::vector< ProteinIdentification >, std::vector< PeptideIdentification > > > &ripped, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides)
Ripping protein/peptide identification according their file origin.
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
void setInitialParameters(const GaussFitResult &result)
sets the initial parameters used by the fit method as initial guess for the Gaussian
void plotTargetDecoyEstimation(std::vector< double > &target, std::vector< double > &decoy)
plots the estimated distribution against target and decoy hits
void store(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.
Generates theoretical spectra with various options.
Definition: TheoreticalSpectrumGenerator.h:63
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
void remove(const String &key)
Remove the entry key or a section key (when suffix is ':')
static double mean(IteratorType begin, IteratorType end)
Calculates the mean of a range of values.
Definition: StatisticFunctions.h:134
String toString() const
Conversion to String.
Management and storage of parameters / INI files.
Definition: Param.h:74
const String & getScoreType() const
Returns the protein score type.
bool isHigherScoreBetter() const
Returns true if a higher score represents a better score.
Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications.
Definition: IDMapper.h:66
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
const std::vector< ProteinGroup > & getProteinGroups() const
Returns the protein groups.
Exception used if an error occurred while fitting a model to a given dataset.
Definition: Exception.h:676
Implements a mixture model of the inverse gumbel and the gauss distribution or a gaussian mixture.
Definition: PosteriorErrorProbabilityModel.h:67
DateTime Class.
Definition: DateTime.h:54
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:321
Used to load and store idXML files.
Definition: IdXMLFile.h:63
void annotate(PeakMap &map, const std::vector< PeptideIdentification > &peptide_ids, const std::vector< ProteinIdentification > &protein_ids, const bool clear_ids=false, const bool mapMS1=false)
Mapping method for peak maps.
Definition: IDMapper.h:96
static double sd(IteratorType begin, IteratorType end, double mean=std::numeric_limits< double >::max())
Calculates the standard deviation of a range of values.
Definition: StatisticFunctions.h:306
Representation of a peptide hit.
Definition: PeptideHit.h:54