OpenMS  3.0.0
ROCCurve.h
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34 
35 #pragma once
36 
37 #include <OpenMS/config.h>
38 #include <OpenMS/CONCEPT/Types.h>
39 
40 #include <list>
41 #include <vector>
42 
43 namespace OpenMS
44 {
45  namespace Math
46  {
54  class OPENMS_DLLAPI ROCCurve
55  {
56 public:
57 
58  // @name Constructors and Destructors
59  // @{
61  ROCCurve();
62 
64  explicit ROCCurve(const std::vector<std::pair<double,bool>> & pairs);
65 
67  virtual ~ROCCurve() = default;
68 
70  ROCCurve(const ROCCurve & source);
71  // @}
72 
73  // @name Operators
74  // @{
76  ROCCurve & operator=(const ROCCurve & source);
77  // @}
78 
79  // @name Accessors
80  // @{
82  void insertPair(double score, bool clas);
83 
85  double AUC();
86 
88  double rocN(Size N);
89 
91  std::vector<std::pair<double, double> > curve(UInt resolution = 10);
92 
95  double cutoffPos(double fraction = 0.95);
96 
99  double cutoffNeg(double fraction = 0.95);
100 
101  // @}
102 
103 private:
105  inline void sort();
106 
108  inline void count();
109 
112  inline double trapezoidal_area(double x1, double x2, double y1, double y2);
113 
115  class OPENMS_DLLAPI simsortdec
116  {
117 public:
118 
119  bool operator()(const std::pair<double, bool> & a, const std::pair<double, bool> & b)
120  {
121  return b.first < a.first;
122  }
123 
124  };
125 
126 
127  std::vector<std::pair<double, bool> > score_clas_pairs_;
128 
130 
132 
133  bool sorted_;
134  };
135  }
136 }
OpenMS::SpectrumAlignment::getSpectrumAlignment
void getSpectrumAlignment(std::vector< std::pair< Size, Size > > &alignment, const SpectrumType1 &s1, const SpectrumType2 &s2) const
Definition: SpectrumAlignment.h:88
OpenMS::DataArrays::IntegerDataArray
Integer data array class.
Definition: DataArrays.h:52
OpenMS::ProteinIdentification::SearchParameters::digestion_enzyme
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:273
OpenMS::ProgressLogger::setProgress
void setProgress(SignedSize value) const
Sets the current progress.
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::TextFile::addLine
void addLine(const StringType &line)
Definition: TextFile.h:112
OpenMS::Deisotoper::deisotopeAndSingleCharge
static void deisotopeAndSingleCharge(MSSpectrum &spectrum, double fragment_tolerance, bool fragment_unit_ppm, int min_charge=1, int max_charge=3, bool keep_only_deisotoped=false, unsigned int min_isopeaks=3, unsigned int max_isopeaks=10, bool make_single_charged=true, bool annotate_charge=false, bool annotate_iso_peak_count=false, bool use_decreasing_model=true, unsigned int start_intensity_check=2, bool add_up_intensity=false)
Detect isotopic clusters in a mass spectrum.
TextFile.h
OpenMS::Math::ROCCurve::simsortdec
predicate for sort()
Definition: ROCCurve.h:115
Size
ListUtilsIO.h
OpenMS::Normalizer
Normalizes the peak intensities spectrum-wise.
Definition: Normalizer.h:57
OpenMS::PeptideIndexing::PEPTIDE_IDS_EMPTY
Definition: PeptideIndexing.h:125
OpenMS::FalseDiscoveryRate::apply
void apply(std::vector< PeptideIdentification > &fwd_ids, std::vector< PeptideIdentification > &rev_ids) const
Calculates the FDR of two runs, a forward run and a decoy run on peptide level.
VersionInfo.h
double
OpenMS::toString
const std::string & toString(const DriftTimeUnit value)
OpenMS::Param::setValue
void setValue(const std::string &key, const ParamValue &value, const std::string &description="", const std::vector< std::string > &tags=std::vector< std::string >())
Sets a value.
OpenMS::Internal::AreaIterator
Forward iterator for an area of peaks in an experiment.
Definition: AreaIterator.h:57
OpenMS::AASequence::getPrefix
AASequence getPrefix(Size index) const
returns a peptide sequence of the first index residues
OpenMS::IdXMLFile::store
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.
OpenMS::ResidueModification
Representation of a modification on an amino acid residue.
Definition: ResidueModification.h:78
OpenMS::ProteaseDigestion::setEnzyme
void setEnzyme(const String &name)
Sets the enzyme for the digestion (by name)
Types.h
OpenMS::FASTAFile::FASTAEntry::identifier
String identifier
Definition: FASTAFile.h:73
OpenMS::DigestionEnzymeDB::getInstance
static InstanceType * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
OpenMS::MSExperiment::sortSpectra
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
OpenMS::String::substitute
String & substitute(char from, char to)
Replaces all occurrences of the character from by the character to.
OpenMS::FASTAFile
This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusua...
Definition: FASTAFile.h:60
OpenMS::WindowMower
WindowMower augments the highest peaks in a sliding or jumping window.
Definition: WindowMower.h:54
OpenMS::MSExperiment::areaEndConst
ConstAreaIterator areaEndConst() const
Returns an non-mutable invalid area iterator marking the end of an area.
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::Peak1D::setMZ
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:119
OpenMS::Constants::k
const double k
Definition: Constants.h:153
OpenMS::FASTAFile::FASTAEntry::sequence
String sequence
Definition: FASTAFile.h:75
OpenMS::ProteinIdentification::SearchParameters::missed_cleavages
UInt missed_cleavages
The number of allowed missed cleavages.
Definition: ProteinIdentification.h:268
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment::begin
Iterator begin()
Definition: MSExperiment.h:150
OpenMS::EmpiricalFormula::getMonoWeight
double getMonoWeight() const
returns the mono isotopic weight of the formula (includes proton charges)
OpenMS::WindowMower::filterPeakSpectrum
void filterPeakSpectrum(PeakSpectrum &spectrum)
MzMLFile.h
Int
RNPxlReport.h
OpenMS::PeptideIdentification::setRT
void setRT(double rt)
sets the RT of the MS2 spectrum where the identification occurred
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::SpectrumSettings::getPrecursors
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
OpenMS::RNPxlModificationMassesResult::mod_combinations
std::map< String, std::set< String > > mod_combinations
empirical formula -> nucleotide formula(s) (formulas if modifications lead to ambiguities)
Definition: RNPxlModificationsGenerator.h:52
OpenMS::TextFile
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
OpenMS::PeakFileOptions::addMSLevel
void addMSLevel(int level)
adds a desired MS level for peaks to load
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
FeatureXMLFile.h
OpenMS::Constants::c
const double c
Definition: Constants.h:209
OpenMS::ResidueModification::N_TERM
The modification can only be N-terminal on the peptide.
Definition: ResidueModification.h:101
OpenMS::RNPxlReport::annotate
static std::vector< RNPxlReportRow > annotate(const PeakMap &spectra, std::vector< PeptideIdentification > &peptide_ids, double marker_ions_tolerance)
OpenMS::Internal::ClassTest::ratio
double ratio
Recent ratio of numbers, see TOLERANCE_RELATIVE.
HyperScore.h
RNPxlModificationsGenerator.h
OpenMS::AASequence::toString
String toString() const
returns the peptide as string with modifications embedded in brackets
OpenMS::ProgressLogger::startProgress
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
OpenMS::PeptideIndexing::run
ExitCodes run(std::vector< FASTAFile::FASTAEntry > &proteins, std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids)
forward for old interface and pyOpenMS; use other run() methods for more control
OpenMS::AASequence::toUnmodifiedString
String toUnmodifiedString() const
returns the peptide as string without any modifications or (e.g., "PEPTIDER")
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::Math::ROCCurve
ROCCurves show the trade-off in sensitivity and specificity for binary classifiers using different cu...
Definition: ROCCurve.h:54
ResidueDB.h
SpectrumSettings.h
OpenMS::Constants::PROTON_MASS_U
const double PROTON_MASS_U
Definition: Constants.h:116
OPENMS_LOG_WARN
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
OpenMS::ProgressLogger::endProgress
void endProgress() const
Ends the progress display.
RNPxlMarkerIonExtractor.h
Constants.h
OpenMS::FASTAFile::FASTAEntry
FASTA entry type (identifier, description and sequence) The first String corresponds to the identifie...
Definition: FASTAFile.h:71
OpenMS::PeptideIndexing::UNEXPECTED_RESULT
Definition: PeptideIndexing.h:127
OpenMS::String::hasPrefix
bool hasPrefix(const String &string) const
true if String begins with string, false otherwise
OpenMS::String::hasSubstring
bool hasSubstring(const String &string) const
true if String contains the string, false otherwise
OpenMS::EnzymaticDigestion::setMissedCleavages
void setMissedCleavages(Size missed_cleavages)
Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when lo...
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:120
OpenMS::NLargest
NLargest removes all but the n largest peaks.
Definition: NLargest.h:54
OpenMS::PeptideIdentification::setHits
void setHits(const std::vector< PeptideHit > &hits)
Sets the peptide hits.
OpenMS::MSSpectrum::getStringDataArrays
const StringDataArrays & getStringDataArrays() const
Returns a const reference to the string meta data arrays.
OpenMS::ProteinIdentification::SearchParameters::fragment_mass_tolerance_ppm
bool fragment_mass_tolerance_ppm
Mass tolerance unit of fragment ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:270
OpenMS::DateTime::now
static DateTime now()
Returns the current date and time.
OpenMS::EmpiricalFormula::toString
String toString() const
returns the formula as a string (charges are not included)
OpenMS::ListUtils::concatenate
static String concatenate(const std::vector< T > &container, const String &glue="")
Concatenates all elements of the container and puts the glue string between elements.
Definition: ListUtils.h:209
OpenMS::ModificationsDB::getInstance
static ModificationsDB * getInstance()
Returns a pointer to the modifications DB (singleton)
WindowMower.h
OpenMS::ProteinIdentification::SearchParameters::charges
String charges
The allowed charges for the search.
Definition: ProteinIdentification.h:264
OpenMS::SpectrumAlignment
Aligns the peaks of two sorted spectra Method 1: Using a banded (width via 'tolerance' parameter) ali...
Definition: SpectrumAlignment.h:67
RNPxlFragmentAnnotationHelper.h
OpenMS::PeptideIdentification::assignRanks
void assignRanks()
Sorts the hits by score and assigns ranks according to the scores.
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::String::number
static String number(double d, UInt n)
returns a string for d with exactly n decimal places
OpenMS::MSExperiment::addSpectrum
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
OpenMS::ResidueModification::toString
String toString() const
OpenMS::ModifiedPeptideGenerator::applyFixedModifications
static void applyFixedModifications(const MapToResidueType &fixed_mods, AASequence &peptide)
ProteaseDigestion.h
OpenMS::MSExperiment::areaBeginConst
ConstAreaIterator areaBeginConst(CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz) const
Returns a non-mutable area iterator for area.
OpenMS::Normalizer::filterPeakMap
void filterPeakMap(PeakMap &exp) const
OpenMS::PeptideHit::PeakAnnotation::charge
int charge
Definition: PeptideHit.h:86
OpenMS::ProteinIdentification::SearchParameters::variable_modifications
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:267
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProteaseDB.h
OpenMS::Internal::RNPxlFragmentAnnotationHelper::getAnnotatedImmoniumIon
static String getAnnotatedImmoniumIon(char c, const String &fragment_shift_name)
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
OpenMS::PrecursorPurity::computePrecursorPurities
static std::map< String, PurityScores > computePrecursorPurities(const PeakMap &spectra, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm)
compute precursor purity metrics for each MS2 spectrum in a PeakMap This is the main function of this...
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...
StringView.h
OpenMS::ResidueModification::C_TERM
The modification can only be C-terminal on the peptide.
Definition: ResidueModification.h:100
OpenMS::PeptideHit::PeakAnnotation::annotation
String annotation
Definition: PeptideHit.h:85
FASTAFile.h
OpenMS::ProteinIdentification::SearchParameters::db
String db
The used database.
Definition: ProteinIdentification.h:261
OpenMS::String::has
bool has(Byte byte) const
true if String contains the byte, false otherwise
OpenMS::StringView
StringView provides a non-owning view on an existing string.
Definition: StringView.h:55
FeatureMap.h
Param.h
OpenMS::Peak1D::getMZ
CoordinateType getMZ() const
Non-mutable access to m/z.
Definition: Peak1D.h:113
OpenMS::AASequence::size
Size size() const
returns the number of residues
OPENMS_LOG_DEBUG
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
OpenMS::PeptideIdentification::setHigherScoreBetter
void setHigherScoreBetter(bool value)
sets the peptide score orientation
OpenMS::Math::ROCCurve::score_clas_pairs_
std::vector< std::pair< double, bool > > score_clas_pairs_
Definition: ROCCurve.h:127
OpenMS::MorpheusScore::compute
static Result compute(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &exp_spectrum, const PeakSpectrum &theo_spectrum)
returns Morpheus Score, #matched ions, #total ions, #matched intensities, #total fragment intensities...
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::PeptideHit::PeakAnnotation::mz
double mz
Definition: PeptideHit.h:87
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::Internal
Namespace used to hide implementation details from users.
Definition: CompNovoIdentificationBase.h:244
Normalizer.h
OpenMS::PeptideHit::setCharge
void setCharge(Int charge)
sets the charge of the peptide
OpenMS::TheoreticalSpectrumGenerator::getSpectrum
virtual void getSpectrum(PeakSpectrum &spec, const AASequence &peptide, Int min_charge, Int max_charge, Int precursor_charge=0) const
OpenMS::VersionInfo::getVersion
static String getVersion()
Return the version number of OpenMS.
OpenMS::DefaultParamHandler::getParameters
const Param & getParameters() const
Non-mutable access to the parameters.
OpenMS::PeptideHit::PeakAnnotation::intensity
double intensity
Definition: PeptideHit.h:88
OpenMS::DataArrays::StringDataArray
String data array class.
Definition: DataArrays.h:59
OpenMS::ProteinIdentification::SearchParameters::fragment_mass_tolerance
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:269
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:53
OpenMS::PeptideIndexing::ExitCodes
ExitCodes
Exit codes.
Definition: PeptideIndexing.h:121
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::MSSpectrum::sortByPosition
void sortByPosition()
Lexicographically sorts the peaks by their position.
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::PeptideHit::setSequence
void setSequence(const AASequence &sequence)
sets the peptide sequence
OpenMS::ProteinIdentification::SearchParameters::fixed_modifications
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:266
ModificationsDB.h
NLargest.h
OpenMS::FalseDiscoveryRate
Calculates false discovery rates (FDR) from identifications.
Definition: FalseDiscoveryRate.h:77
OpenMS::PeptideHit::setPeakAnnotations
void setPeakAnnotations(std::vector< PeptideHit::PeakAnnotation > frag_annotations)
sets the fragment annotations
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
MSExperiment.h
OpenMS::ProteinIdentification::SearchParameters::precursor_mass_tolerance
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:271
OpenMS::Math::ROCCurve::neg_
UInt neg_
Definition: ROCCurve.h:131
OpenMS::Constants::UserParam::ISOTOPE_ERROR
const std::string ISOTOPE_ERROR
Definition: Constants.h:327
OpenMS::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
OpenMS::TheoreticalSpectrumGenerator
Generates theoretical spectra for peptides with various options.
Definition: TheoreticalSpectrumGenerator.h:68
OpenMS::ModificationsDB::addModification
const ResidueModification * addModification(std::unique_ptr< ResidueModification > new_mod)
Add a new modification to ModificationsDB. If the modification already exists (based on its fullID) i...
OpenMS::Internal::RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToPHFA
static std::vector< PeptideHit::PeakAnnotation > fragmentAnnotationDetailsToPHFA(const String &ion_type, std::map< Size, std::vector< FragmentAnnotationDetail_ > > ion_annotation_details)
conversion of RNPxl annotations to PeptideHit::PeakAnnotation
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::EnzymaticDigestion::digestUnmodified
Size digestUnmodified(const StringView &sequence, std::vector< StringView > &output, Size min_length=1, Size max_length=0) const
Performs the enzymatic digestion of an unmodified sequence.
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::String::substr
String substr(size_t pos=0, size_t n=npos) const
Wrapper for the STL substr() method. Returns a String object with its contents initialized to a subst...
OpenMS::ThresholdMower::filterPeakMap
void filterPeakMap(PeakMap &exp)
OpenMS::ProteaseDigestion
Class for the enzymatic digestion of proteins.
Definition: ProteaseDigestion.h:59
OpenMS::MSExperiment::end
Iterator end()
Definition: MSExperiment.h:160
OpenMS::AASequence::getSuffix
AASequence getSuffix(Size index) const
returns a peptide sequence of the last index residues
OpenMS::FASTAFile::load
void load(const String &filename, std::vector< FASTAEntry > &data) const
loads a FASTA file given by 'filename' and stores the information in 'data' This uses more RAM than r...
OpenMS::Internal::RNPxlFragmentAnnotationHelper::shiftedIonsToString
static String shiftedIonsToString(const std::vector< PeptideHit::PeakAnnotation > &as)
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:84
OpenMS::PeptideIndexing::DATABASE_EMPTY
Definition: PeptideIndexing.h:124
ElementDB.h
OpenMS::PeptideIndexing
Refreshes the protein references for all peptide hits in a vector of PeptideIdentifications and adds ...
Definition: PeptideIndexing.h:113
OpenMS::StringUtils::has
static bool has(const String &this_s, Byte byte)
Definition: StringUtilsSimple.h:142
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::ThresholdMower
ThresholdMower removes all peaks below a threshold.
Definition: ThresholdMower.h:51
PeptideIndexing.h
OpenMS::String::reverse
String & reverse()
inverts the direction of the string
OpenMS::ModificationsDB::getAllSearchModifications
void getAllSearchModifications(std::vector< String > &modifications) const
Collects all modifications that can be used for identification searches.
OpenMS::Math::ROCCurve::pos_
UInt pos_
Definition: ROCCurve.h:129
OpenMS::TextFile::store
void store(const String &filename)
Writes the data to a file.
OpenMS::ModifiedPeptideGenerator::MapToResidueType
Definition: ModifiedPeptideGenerator.h:58
OpenMS::PeakFileOptions::clearMSLevels
void clearMSLevels()
clears the MS levels
OpenMS::ProteinIdentification::SearchParameters::precursor_mass_tolerance_ppm
bool precursor_mass_tolerance_ppm
Mass tolerance unit of precursor ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:272
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
Deisotoper.h
OpenMS::RNPxlReportRowHeader
create header line
Definition: RNPxlReport.h:79
OpenMS::MSExperiment::clear
void clear(bool clear_meta_data)
Clears all data and meta data.
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
MorpheusScore.h
ModifiedPeptideGenerator.h
OPENMS_POSTCONDITION
#define OPENMS_POSTCONDITION(condition, message)
Postcondition macro.
Definition: openms/include/OpenMS/CONCEPT/Macros.h:127
OpenMS::MSExperiment::ConstIterator
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:106
ResidueModification.h
OpenMS::AASequence::fromString
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
TheoreticalSpectrumGenerator.h
OpenMS::RNPxlModificationMassesResult::mod_masses
std::map< String, double > mod_masses
empirical formula -> mass
Definition: RNPxlModificationsGenerator.h:51
OpenMS::ModifiedPeptideGenerator::applyVariableModifications
static void applyVariableModifications(const MapToResidueType &var_mods, const AASequence &peptide, Size max_variable_mods_per_peptide, std::vector< AASequence > &all_modified_peptides, bool keep_original=true)
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::MSSpectrum::getIntegerDataArrays
const IntegerDataArrays & getIntegerDataArrays() const
Returns a const reference to the integer meta data arrays.
OpenMS::Internal::AreaIterator::getRT
CoordinateType getRT() const
returns the retention time of the current scan
Definition: AreaIterator.h:198
SpectrumAlignment.h
OpenMS::ModifiedPeptideGenerator::getModifications
static MapToResidueType getModifications(const StringList &modNames)
Retrieve modifications from strings.
OpenMS::Constants::C13C12_MASSDIFF_U
const double C13C12_MASSDIFF_U
Definition: Constants.h:121
OpenMS::PeptideIndexing::EXECUTION_OK
Definition: PeptideIndexing.h:123
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
OpenMS::PeptideIdentification::setMZ
void setMZ(double mz)
sets the MZ of the MS2 spectrum
FalseDiscoveryRate.h
OpenMS::Math::ROCCurve::simsortdec::operator()
bool operator()(const std::pair< double, bool > &a, const std::pair< double, bool > &b)
Definition: ROCCurve.h:119
OpenMS::Peak1D::getIntensity
IntensityType getIntensity() const
Definition: Peak1D.h:108
OpenMS::PeptideHit::PeakAnnotation
Contains annotations of a peak.
Definition: PeptideHit.h:83
StandardTypes.h
OpenMS::NLargest::filterPeakSpectrum
void filterPeakSpectrum(PeakSpectrum &spectrum)
OpenMS::String::toInt
Int toInt() const
Conversion to int.
OpenMS::RNPxlModificationsGenerator::initModificationMassesRNA
static RNPxlModificationMassesResult initModificationMassesRNA(StringList target_nucleotides, StringList nt_groups, std::set< char > can_xl, StringList mappings, StringList modifications, String sequence_restriction, bool cysteine_adduct, Int max_length=4)
PrecursorPurity.h
OpenMS::Math::ROCCurve::sorted_
bool sorted_
Definition: ROCCurve.h:133
OpenMS::HyperScore::compute
static double compute(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &exp_spectrum, const PeakSpectrum &theo_spectrum)
compute the (ln transformed) X!Tandem HyperScore 1. the dot product of peak intensities between match...
OpenMS::MzMLFile::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h
OpenMS::Internal::RNPxlFragmentAnnotationHelper::addShiftedPeakFragmentAnnotation_
static void addShiftedPeakFragmentAnnotation_(const std::map< Size, std::vector< FragmentAnnotationDetail_ >> &shifted_b_ions, const std::map< Size, std::vector< FragmentAnnotationDetail_ >> &shifted_y_ions, const std::map< Size, std::vector< FragmentAnnotationDetail_ >> &shifted_a_ions, const std::vector< PeptideHit::PeakAnnotation > &shifted_immonium_ions, const std::vector< PeptideHit::PeakAnnotation > &annotated_marker_ions, const std::vector< PeptideHit::PeakAnnotation > &annotated_precursor_ions, std::vector< PeptideHit::PeakAnnotation > &fas)
OpenMS::RNPxlModificationMassesResult
Definition: RNPxlModificationsGenerator.h:49
OpenMS::Internal::RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_
Single fragment annotation.
Definition: RNPxlFragmentAnnotationHelper.h:62
OpenMS::PeptideIdentification::setScoreType
void setScoreType(const String &type)
sets the peptide score type
MSSpectrum.h
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
ThresholdMower.h
OpenMS::PeptideHit::setScore
void setScore(double score)
sets the PSM score
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55