OpenMS  2.4.0
IDRipper.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Immanuel Luhn $
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34 #pragma once
35 
39 
40 
41 namespace OpenMS
42 {
52  class OPENMS_DLLAPI IDRipper :
53  public DefaultParamHandler
54  {
55 public:
56 
58  IDRipper();
59 
61  ~IDRipper() override;
62 
73  void rip(std::map<String, std::pair<std::vector<ProteinIdentification>, std::vector<PeptideIdentification> > > & ripped, std::vector<ProteinIdentification> & proteins, std::vector<PeptideIdentification> & peptides);
74 
75 private:
76 
77  //Not implemented
79  IDRipper(const IDRipper & rhs);
80 
81  // Not implemented
83  IDRipper & operator=(const IDRipper & rhs);
84 
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);
90  void getProteinIdentification_(ProteinIdentification & result, PeptideIdentification pep_ident, std::vector<ProteinIdentification> & prot_idents);
91  };
92 
93 } // namespace OpenMS
94 
DefaultParamHandler.h
OpenMS::SpectrumAlignment::getSpectrumAlignment
void getSpectrumAlignment(std::vector< std::pair< Size, Size > > &alignment, const SpectrumType1 &s1, const SpectrumType2 &s2) const
Definition: SpectrumAlignment.h:86
OpenMS::Math::GaussFitter
Implements a fitter for Gaussian functions.
Definition: GaussFitter.h:58
OpenMS::PeptideHit::getCharge
Int getCharge() const
returns the charge of the peptide
OpenMS::Math::PosteriorErrorProbabilityModel::extractAndTransformScores
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
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:150
OpenMS::Param::copy
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
IDRipper.h
OpenMS::Normalizer
Normalizes the peak intensities spectrum-wise.
Definition: Normalizer.h:57
OpenMS::DPosition::setX
void setX(CoordinateType c)
Name mutator for the first dimension. Only for DPosition<2>, for visualization.
Definition: DPosition.h:164
OpenMS::ProteinIdentification::getIndistinguishableProteins
const std::vector< ProteinGroup > & getIndistinguishableProteins() const
Returns the indistinguishable proteins.
OpenMS::Math::median
static double median(IteratorType begin, IteratorType end, bool sorted=false)
Calculates the median of a range of values.
Definition: StatisticFunctions.h:152
OpenMS::ProteinIdentification::getSignificanceThreshold
double getSignificanceThreshold() const
Returns the protein significance threshold value.
OpenMS::PeptideHit::getSequence
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
GaussFitter.h
Int
OpenMS::File::basename
static String basename(const String &file)
Returns the basename of the file (without the path).
OpenMS::Param::setValue
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
OpenMS::Math::GaussFitter::GaussFitResult
struct of parameters of a Gaussian distribution
Definition: GaussFitter.h:63
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:57
OpenMS::Math::GaussFitter::fit
GaussFitResult fit(std::vector< DPosition< 2 > > &points) const
Fits a Gaussian distribution to the given data points.
OpenMS::Exception::Precondition
Precondition failed exception.
Definition: Exception.h:166
OpenMS::String::trim
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
MzMLFile.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::AASequence::getMonoWeight
double getMonoWeight(Residue::ResidueType type=Residue::Full, Int charge=0) const
IdXMLFile.h
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:53
OpenMS::ProteinIdentification::findHit
std::vector< ProteinHit >::iterator findHit(const String &accession)
Finds a protein hit by accession (returns past-the-end iterator if not found)
LOG_INFO
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
StatisticFunctions.h
OpenMS::Param::getValue
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
OpenMS::AASequence::toString
String toString() const
returns the peptide as string with modifications embedded in brackets
OpenMS::Normalizer::filterSpectrum
void filterSpectrum(SpectrumType &spectrum) const
Definition: Normalizer.h:86
OpenMS::TheoreticalSpectrumGenerator::getSpectrum
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
OpenMS::Constants::PROTON_MASS_U
const double PROTON_MASS_U
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
Constants.h
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::DateTime::now
static DateTime now()
Returns the current date and time.
OpenMS::File::writable
static bool writable(const String &file)
Return true if the file is writable.
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS::Math::PosteriorErrorProbabilityModel::fit
bool fit(std::vector< double > &search_engine_scores)
fits the distributions to the data points(search_engine_scores). Estimated parameters for the distrib...
OpenMS::Exception::InvalidParameter
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:347
OpenMS::SpectrumAlignment
Aligns the peaks of two sorted spectra Method 1: Using a banded (width via 'tolerance' parameter) ali...
Definition: SpectrumAlignment.h:65
OpenMS::IDRipper
Ripping protein/peptide identification according their file origin.
Definition: IDRipper.h:52
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MSExperiment::Iterator
std::vector< SpectrumType >::iterator Iterator
Mutable iterator.
Definition: MSExperiment.h:111
LOG_DEBUG
#define LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:458
OpenMS::Math::Histogram
Representation of a histogram.
Definition: Histogram.h:63
LOG_WARN
#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
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
OpenMS::DataValue
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
OpenMS::Param::exists
bool exists(const String &key) const
Tests if a parameter is set (expecting its fully qualified name, e.g., TextExporter:1:proteins_only)
OpenMS::MzMLFile::load
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
OpenMS::ProteinIdentification::getHits
const std::vector< ProteinHit > & getHits() const
Returns the protein hits.
ProteinIdentification.h
OpenMS::Math::PosteriorErrorProbabilityModel::updateScores
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
OpenMS::String::split
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
Normalizer.h
OpenMS::DPosition::setY
void setY(CoordinateType c)
Name mutator for the second dimension. Only for DPosition<2>, for visualization.
Definition: DPosition.h:171
OpenMS::DefaultParamHandler::getParameters
const Param & getParameters() const
Non-mutable access to the parameters.
OpenMS::PeptideHit::extractProteinAccessionsSet
std::set< String > extractProteinAccessionsSet() const
extracts the set of non-empty protein accessions from peptide evidences
OpenMS::IDRipper::rip
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.
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
OpenMS::DPosition< 2 >
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
IDMapper.h
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
OpenMS::Math::GaussFitter::setInitialParameters
void setInitialParameters(const GaussFitResult &result)
sets the initial parameters used by the fit method as initial guess for the Gaussian
MSExperiment.h
OpenMS::Math::PosteriorErrorProbabilityModel::plotTargetDecoyEstimation
void plotTargetDecoyEstimation(std::vector< double > &target, std::vector< double > &decoy)
plots the estimated distribution against target and decoy hits
OpenMS::IdXMLFile::store
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.
Histogram.h
OpenMS::TheoreticalSpectrumGenerator
Generates theoretical spectra with various options.
Definition: TheoreticalSpectrumGenerator.h:63
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::Param::remove
void remove(const String &key)
Remove the entry key or a section key (when suffix is ':')
OpenMS::Math::mean
static double mean(IteratorType begin, IteratorType end)
Calculates the mean of a range of values.
Definition: StatisticFunctions.h:134
OpenMS::DataValue::toString
String toString() const
Conversion to String.
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:74
OpenMS::ProteinIdentification::getScoreType
const String & getScoreType() const
Returns the protein score type.
TheoreticalSpectrumGenerator.h
OpenMS::ProteinIdentification::isHigherScoreBetter
bool isHigherScoreBetter() const
Returns true if a higher score represents a better score.
SpectrumAlignment.h
PeptideIdentification.h
OpenMS::IDMapper
Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications.
Definition: IDMapper.h:66
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::ProteinIdentification::getProteinGroups
const std::vector< ProteinGroup > & getProteinGroups() const
Returns the protein groups.
OpenMS::Exception::UnableToFit
Exception used if an error occurred while fitting a model to a given dataset.
Definition: Exception.h:676
OpenMS::Math::PosteriorErrorProbabilityModel
Implements a mixture model of the inverse gumbel and the gauss distribution or a gaussian mixture.
Definition: PosteriorErrorProbabilityModel.h:67
PosteriorErrorProbabilityModel.h
StandardTypes.h
OpenMS::DateTime
DateTime Class.
Definition: DateTime.h:54
File.h
TOPPBase.h
OpenMS::Math::absdev
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
MSSpectrum.h
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63
OpenMS::IDMapper::annotate
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
OpenMS::Math::sd
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
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54