OpenMS  2.5.0
MissedCleavages.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Swenja Wagner, Patricia Scheil $
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34 
35 
36 #pragma once
37 
38 #include <OpenMS/QC/QCBase.h>
39 
40 #include <vector>
41 #include <map>
42 namespace OpenMS
43 {
44  class FeatureMap;
55  class OPENMS_DLLAPI MissedCleavages : public QCBase
56  {
57  public:
59  MissedCleavages() = default;
60 
62  virtual ~MissedCleavages() = default;
63 
73  void compute(FeatureMap& fmap);
74 
76  const String& getName() const override;
77 
79  const std::vector<std::map<UInt32, UInt32>>& getResults() const;
80 
85  QCBase::Status requires() const override;
86 
87  private:
89  const String name_ = "MissedCleavages";
90 
92  std::vector<std::map<UInt32, UInt32>> mc_result_;
93  };
94 } // namespace OpenMS
OpenMS::PeptideIdentification::assignRanks
void assignRanks()
Sorts the hits by score and assigns ranks according to the scores.
SIPPeptide::correlation_maxima
vector< RateScorePair > correlation_maxima
Definition: MetaProSIP.cpp:134
CoarseIsotopePatternGenerator.h
MetaProSIPXICExtraction::extractXICs
static vector< vector< double > > extractXICs(double seed_rt, vector< double > xic_mzs, double mz_toelrance_ppm, double rt_tolerance_s, const PeakMap &peak_map)
Definition: MetaProSIP.cpp:1824
FASTAFile.h
OpenMS::Internal::DIntervalBase::minPosition
PositionType const & minPosition() const
Accessor to minimum position.
Definition: DIntervalBase.h:124
SIPPeptide::mz_theo
double mz_theo
theoretical mz
Definition: MetaProSIP.cpp:116
OpenMS::SVOutStream
Stream class for writing to comma/tab/...-separated values files.
Definition: SVOutStream.h:54
MetaProSIPDecomposition::calculateDecompositionWeightsIsotopicPatterns
static Int calculateDecompositionWeightsIsotopicPatterns(Size n_bins, const vector< double > &isotopic_intensities, const IsotopePatterns &patterns, MapRateToScoreType &map_rate_to_decomposition_weight, SIPPeptide &sip_peptide)
> Perform the decomposition
Definition: MetaProSIP.cpp:1256
RIALess::operator()
bool operator()(const SIPIncorporation &a, const SIPIncorporation &b) const
Definition: MetaProSIP.cpp:187
OpenMS::IsotopeDistribution::clear
void clear()
clears the distribution
OpenMS::String::number
static String number(double d, UInt n)
returns a string for d with exactly n decimal places
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
SIPPeptide::explained_TIC_fraction
double explained_TIC_fraction
fraction of the MS2 TIC that is explained by the maximum correlating decomposition weights
Definition: MetaProSIP.cpp:142
OpenMS::Param::setValue
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
OpenMS::Peak2D
A 2-dimensional raw data point or peak.
Definition: Peak2D.h:54
OpenMS::MSExperiment::updateRanges
void updateRanges() override
Updates minimum and maximum position/intensity.
MetaProSIPDecomposition::calculateIsotopePatternsFor15NRangeOfAveraginePeptide
static IsotopePatterns calculateIsotopePatternsFor15NRangeOfAveraginePeptide(double mass)
Definition: MetaProSIP.cpp:1667
OpenMS::PeptideIdentification::setHits
void setHits(const std::vector< PeptideHit > &hits)
Sets the peptide hits.
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:82
OpenMS::MSSpectrum::MZBegin
Iterator MZBegin(CoordinateType mz)
Binary search for peak range begin.
OpenMS::PeptideHit::getCharge
Int getCharge() const
returns the charge of the peptide
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
SIPPeptide::accessions
vector< String > accessions
protein accessions of the peptide
Definition: MetaProSIP.cpp:112
OpenMS::Constants::k
const double k
MetaProSIPDecomposition::calculateIsotopePatternsFor2HRangeOfAveraginePeptide
static IsotopePatterns calculateIsotopePatternsFor2HRangeOfAveraginePeptide(double mass)
Definition: MetaProSIP.cpp:1742
MetaProSIPXICExtraction
Definition: MetaProSIP.cpp:1821
OpenMS::BaseFeature::setPeptideIdentifications
void setPeptideIdentifications(const std::vector< PeptideIdentification > &peptides)
sets the PeptideIdentification vector
File.h
SIPPeptide::non_zero_decomposition_coefficients
Size non_zero_decomposition_coefficients
decomposition coefficients significantly larger than 0
Definition: MetaProSIP.cpp:146
OpenMS::TextFile
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
OpenMS::FASTAFile::load
static void load(const String &filename, std::vector< FASTAEntry > &data)
loads a FASTA file given by 'filename' and stores the information in 'data'
SIPPeptide::unique
bool unique
if the peptide is unique and therefor identifies the protein umambigously
Definition: MetaProSIP.cpp:114
PeakPickerHiRes.h
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::Residue::Full
with N-terminus and C-terminus
Definition: Residue.h:152
OpenMS::AASequence::getFormula
EmpiricalFormula getFormula(Residue::ResidueType type=Residue::Full, Int charge=0) const
returns the formula of the peptide
OpenMS::Peak1D::setMZ
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:121
OpenMS::Peak2D::setMZ
void setMZ(CoordinateType coordinate)
Mutable access to the m/z coordinate (index 1)
Definition: Peak2D.h:202
OpenMS::Peak2D::setIntensity
void setIntensity(IntensityType intensity)
Non-mutable access to the data point intensity (height)
Definition: Peak2D.h:172
MetaProSIPReporting
Definition: MetaProSIP.cpp:361
OpenMS::MissedCleavages
This class is a metric for the QualityControl TOPP Tool.
Definition: MissedCleavages.h:55
MetaProSIPDecomposition::calculateIsotopePatternsFor13CRangeOfAveraginePeptide
static IsotopePatterns calculateIsotopePatternsFor13CRangeOfAveraginePeptide(double mass)
Definition: MetaProSIP.cpp:1706
ElementDB.h
RIALess
Definition: MetaProSIP.cpp:184
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:127
OpenMS::IsotopeDistribution::insert
void insert(const Peak1D::CoordinateType &mass, const Peak1D::IntensityType &intensity)
Definition: IsotopeDistribution.h:214
OpenMS::TextFile::begin
ConstIterator begin() const
Gives access to the underlying text buffer.
SIPIncorporation::rate
double rate
rate
Definition: MetaProSIP.cpp:97
QProcess
OPENMS_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::PeptideHit::getSequence
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS::MSSpectrum::ConstIterator
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:104
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.
MetaProSIPXICExtraction::extractXICsOfIsotopeTraces
static vector< double > extractXICsOfIsotopeTraces(Size element_count, double mass_diff, double mz_tolerance_ppm, double rt_tolerance_s, double seed_rt, double seed_mz, double seed_charge, const PeakMap &peak_map, const double min_corr_mono=-1.0)
Definition: MetaProSIP.cpp:1891
OpenMS::AASequence::toString
String toString() const
returns the peptide as string with modifications embedded in brackets
SizeLess
Definition: MetaProSIP.cpp:164
OpenMS::Peak1D::setIntensity
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:112
MetaProSIPReporting::writeHTML
static void writeHTML(const String &qc_output_directory, const String &file_suffix, const String &file_extension, const vector< SIPPeptide > &sip_peptides)
Definition: MetaProSIP.cpp:545
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
MapRateToScoreType
map< double, double > MapRateToScoreType
Definition: MetaProSIP.cpp:84
NonNegativeLeastSquaresSolver.h
SIPPeptide::decomposition_map
MapRateToScoreType decomposition_map
Definition: MetaProSIP.cpp:136
SIPPeptide::feature_rt
double feature_rt
measurement time of feature apex [s]
Definition: MetaProSIP.cpp:122
MetaProSIPDecomposition::calculateIsotopePatternsFor18ORangeOfAveraginePeptide
static IsotopePatterns calculateIsotopePatternsFor18ORangeOfAveraginePeptide(double mass)
Definition: MetaProSIP.cpp:1780
OpenMS::MSExperiment::clear
void clear(bool clear_meta_data)
Clears all data and meta data.
OpenMS::TextFile::ConstIterator
std::vector< String >::const_iterator ConstIterator
Non-mutable iterator.
Definition: TextFile.h:56
OpenMS::PeptideHit::setCharge
void setCharge(Int charge)
sets the charge of the peptide
OpenMS::MSExperiment::const_iterator
Base::const_iterator const_iterator
Definition: MSExperiment.h:125
OpenMS::FeatureMap::updateRanges
void updateRanges() override
Updates minimum and maximum position/intensity.
OpenMS::Internal::AreaIterator
Forward iterator for an area of peaks in an experiment.
Definition: AreaIterator.h:57
OpenMS::MSExperiment::getMinRT
CoordinateType getMinRT() const
returns the minimal retention time value
OpenMS::ThresholdMower::filterPeakMap
void filterPeakMap(PeakMap &exp)
MetaProSIPClustering
Definition: MetaProSIP.cpp:265
SequenceLess::operator()
bool operator()(const pair< SIPPeptide, Size > &a, const pair< SIPPeptide, Size > &b) const
Definition: MetaProSIP.cpp:177
double
SIPPeptide::mass_theo
double mass_theo
uncharged theoretical mass
Definition: MetaProSIP.cpp:118
CubicSpline2d.h
OpenMS::MSSpectrum::setMSLevel
void setMSLevel(UInt ms_level)
Sets the MS level.
OpenMS::Internal::AreaIterator::getRT
CoordinateType getRT() const
returns the retention time of the current scan
Definition: AreaIterator.h:198
FeatureMap.h
OpenMS::AASequence::fromString
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
SIPPeptide::patterns
IsotopePatterns patterns
Definition: MetaProSIP.cpp:156
OpenMS::PeptideIdentification::insertHit
void insertHit(const PeptideHit &hit)
Appends a peptide hit.
MetaProSIPReporting::createBinnedPeptideRIAData_
static void createBinnedPeptideRIAData_(const Size n_heatmap_bins, const vector< vector< SIPPeptide > > &sip_clusters, vector< vector< double > > &binned_peptide_ria, vector< String > &cluster_labels)
Definition: MetaProSIP.cpp:1226
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:144
MzMLFile.h
SIPIncorporation::abundance
double abundance
abundance of isotopologue
Definition: MetaProSIP.cpp:101
SIPPeptide::mass_diff
double mass_diff
Definition: MetaProSIP.cpp:130
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::PeakFileOptions::setMSLevels
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
int
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::TextFile::end
ConstIterator end() const
Gives access to the underlying text buffer.
MetaProSIPReporting::plotScoresAndWeights
static void plotScoresAndWeights(const String &output_dir, const String &tmp_path, const String &file_suffix, const String &file_extension, const vector< SIPPeptide > &sip_peptides, double score_plot_yaxis_min, Size debug_level=0, const QString &executable=QString("R"))
Definition: MetaProSIP.cpp:666
OpenMS::MSSpectrum::sortByPosition
void sortByPosition()
Lexicographically sorts the peaks by their position.
OpenMS::Peak1D::getIntensity
IntensityType getIntensity() const
Definition: Peak1D.h:110
SIPPeptide::RR
double RR
R squared of NNLS fit.
Definition: MetaProSIP.cpp:140
RIntegration::checkRDependencies
static bool checkRDependencies(const String &tmp_path, StringList package_names, const QString &executable=QString("R"))
Definition: MetaProSIP.cpp:1935
OpenMS::Peak1D::getMZ
CoordinateType getMZ() const
Non-mutable access to m/z.
Definition: Peak1D.h:115
Normalizer.h
OpenMS::EmpiricalFormula::getIsotopeDistribution
IsotopeDistribution getIsotopeDistribution(const IsotopePatternGenerator &method) const
returns the isotope distribution of the formula The details of the calculation of the isotope distrib...
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
SpectrumAlignment.h
OpenMS::CubicSpline2d::derivatives
double derivatives(double x, unsigned order) const
evaluates derivative of spline at position x
OpenMS::PeptideIdentification::setHigherScoreBetter
void setHigherScoreBetter(bool value)
sets the peptide score orientation
OpenMS::AASequence::getMonoWeight
double getMonoWeight(Residue::ResidueType type=Residue::Full, Int charge=0) const
RateScorePair
Definition: MetaProSIP.cpp:88
SIPIncorporation
datastructure for reporting an incorporation event
Definition: MetaProSIP.cpp:95
SIPPeptide
datastructure for reporting a peptide with one or more incorporation rates comparator for vectors of ...
Definition: MetaProSIP.cpp:108
MetaProSIPClustering::getRIAClusterCenter
static vector< double > getRIAClusterCenter(const vector< SIPPeptide > &sip_peptides, bool debug=false)
Definition: MetaProSIP.cpp:268
OpenMS::MSExperiment::areaEndConst
ConstAreaIterator areaEndConst() const
Returns an non-mutable invalid area iterator marking the end of an area.
SIPPeptide::correlation_map
MapRateToScoreType correlation_map
Definition: MetaProSIP.cpp:138
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
FeatureXMLFile.h
OpenMS::EmpiricalFormula::getNumberOf
SignedSize getNumberOf(const Element *element) const
returns the number of atoms for a certain element (can be negative)
Feature.h
OpenMS::AASequence::toUnmodifiedString
String toUnmodifiedString() const
returns the peptide as string without any modifications or (e.g., "PEPTIDER")
OpenMS::QCBase
This class serves as an abstract base class for all QC classes.
Definition: QCBase.h:52
OpenMS::MSExperiment::ConstIterator
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
OpenMS::MSExperiment::getMaxRT
CoordinateType getMaxRT() const
returns the maximal retention time value
OpenMS::Internal::ClassTest::ratio
double ratio
Recent ratio of numbers, see TOLERANCE_RELATIVE.
OpenMS::String::concatenate
void concatenate(StringIterator first, StringIterator last, const String &glue="")
Concatenates all elements from first to last-1 and inserts glue between the elements.
Definition: String.h:466
OpenMS::PeptideIdentification::getHits
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
OpenMS::Math::pearsonCorrelationCoefficient
static double pearsonCorrelationCoefficient(IteratorType1 begin_a, IteratorType1 end_a, IteratorType2 begin_b, IteratorType2 end_b)
Calculates the Pearson correlation coefficient for the values in [begin_a, end_a) and [begin_b,...
Definition: StatisticFunctions.h:505
RIntegration
Definition: MetaProSIP.cpp:1931
SIPIncorporation::correlation
double correlation
correlation coefficient
Definition: MetaProSIP.cpp:99
OpenMS::ElementDB::getElement
const Element * getElement(const String &name) const
OpenMS::Peak2D::setRT
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
SIPPeptide::score
double score
search engine score or q-value if fdr filtering is applied
Definition: MetaProSIP.cpp:120
OpenMS::Constants::PROTON_MASS_U
const double PROTON_MASS_U
Constants.h
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
MetaProSIPDecomposition::getNumberOfLabelingElements
static Size getNumberOfLabelingElements(const String &labeling_element, const AASequence &peptide)
Definition: MetaProSIP.cpp:1409
MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange
static IsotopePatterns calculateIsotopePatternsFor2HRange(const AASequence &peptide, Size additional_isotopes=5)
Definition: MetaProSIP.cpp:1524
OpenMS::CubicSpline2d
cubic spline interpolation as described in R.L. Burden, J.D. Faires, Numerical Analysis,...
Definition: CubicSpline2d.h:53
ModificationsDB.h
MetaProSIPReporting::plotHeatMap
static void plotHeatMap(const String &output_dir, const String &tmp_path, const String &file_suffix, const String &file_extension, const vector< vector< double > > &binned_ria, vector< String > class_labels, Size debug_level=0, const QString &executable=QString("R"))
Definition: MetaProSIP.cpp:364
OPENMS_LOG_DEBUG
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
Param.h
OpenMS::IsotopeDistribution::set
void set(const ContainerType &distribution)
overwrites the container which holds the distribution using distribution
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::PeptideHit::setSequence
void setSequence(const AASequence &sequence)
sets the peptide sequence
MetaProSIPXICExtraction::correlateXICsToMono
static vector< double > correlateXICsToMono(const vector< vector< double > > &xics)
Definition: MetaProSIP.cpp:1878
OpenMS::QCBase::Status
Storing a status of available/needed inputs (i.e. a set of Requires) as UInt64.
Definition: QCBase.h:118
OpenMS::String::toUpper
String & toUpper()
Converts the string to uppercase.
TOPPBase.h
SIPPeptide::global_LR
double global_LR
labeling ratio for the whole spectrum used to detect global drifts. 13C/(12C+13C) intensities....
Definition: MetaProSIP.cpp:132
MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange
static IsotopePatterns calculateIsotopePatternsFor18ORange(const AASequence &peptide, Size additional_isotopes=5)
Definition: MetaProSIP.cpp:1595
OpenMS::TextFile::addLine
void addLine(const StringType &line)
Definition: TextFile.h:112
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
SIPPeptide::incorporations
vector< SIPIncorporation > incorporations
Definition: MetaProSIP.cpp:154
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::String::random
static String random(UInt length)
returns a random string of the given length. It consists of [0-9a-zA-Z]
QCBase.h
TextFile.h
MetaProSIPDecomposition
Definition: MetaProSIP.cpp:1252
SIPPeptide::feature_type
String feature_type
used to distinguish features from FeatureFinder, or synthetised from ids or averagine ids in reportin...
Definition: MetaProSIP.cpp:144
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
SIPPeptide::feature_mz
double feature_mz
mz of feature apex [s]
Definition: MetaProSIP.cpp:124
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...
StatisticFunctions.h
IsotopePattern
pair< double, vector< double > > IsotopePattern
Definition: MetaProSIP.cpp:85
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::PeptideHit::getScore
double getScore() const
returns the PSM score
SVOutStream.h
seqan::find
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
GaussModel.h
SIPPeptide::reconstruction_monoistopic
vector< double > reconstruction_monoistopic
signal reconstruction of natural peptide (at mono-isotopic peak)
Definition: MetaProSIP.cpp:150
OpenMS::MSExperiment::sortSpectra
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
OpenMS::TIC
Definition: TIC.h:52
OpenMS::String::NONE
Definition: String.h:81
MetaProSIPReporting::createPeptideCentricCSVReport
static void createPeptideCentricCSVReport(const String &in_mzML, const String &file_extension, vector< vector< SIPPeptide > > &sippeptide_cluster, ofstream &os, map< String, String > &proteinid_to_description, String qc_output_directory, String file_suffix, bool report_natural_peptides)
Definition: MetaProSIP.cpp:1102
OpenMS::MSSpectrum::MZEnd
Iterator MZEnd(CoordinateType mz)
Binary search for peak range end (returns the past-the-end iterator)
OpenMS::String
A more convenient string class.
Definition: String.h:58
MassDecomposition.h
Element.h
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:64
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54
SIPPeptide::accumulated
PeakSpectrum accumulated
Definition: MetaProSIP.cpp:152
OpenMS::Math::sum
static double sum(IteratorType begin, IteratorType end)
Calculates the sum of a range of values.
Definition: StatisticFunctions.h:120
SequenceLess
Definition: MetaProSIP.cpp:174
OpenMS::TextFile::store
void store(const String &filename)
Writes the data to a file.
OpenMS::Math::mean
static double mean(IteratorType begin, IteratorType end)
Calculates the mean of a range of values.
Definition: StatisticFunctions.h:133
SIPPeptide::reconstruction
PeakSpectrum reconstruction
signal reconstruction (debugging)
Definition: MetaProSIP.cpp:148
OpenMS::ThresholdMower
ThresholdMower removes all peaks below a threshold.
Definition: ThresholdMower.h:51
OpenMS::MSExperiment::RTBegin
ConstIterator RTBegin(CoordinateType rt) const
Fast search for spectrum range begin.
OpenMS::DBoundingBox< 2 >
OpenMS::CoarseIsotopePatternGenerator::estimateFromPeptideWeight
IsotopeDistribution estimateFromPeptideWeight(double average_weight)
Estimate Peptide Isotopedistribution from weight and number of isotopes that should be reported.
OpenMS::Element::setIsotopeDistribution
void setIsotopeDistribution(const IsotopeDistribution &isotopes)
sets the isotope distribution of the element
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Matrix< double >
OpenMS::MSExperiment::empty
bool empty() const
Definition: MSExperiment.h:137
OpenMS::IsotopeDistribution::getContainer
const ContainerType & getContainer() const
returns the container which holds the distribution
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::String::substitute
String & substitute(char from, char to)
Replaces all occurrences of the character from by the character to.
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
IsotopePatterns
vector< IsotopePattern > IsotopePatterns
Definition: MetaProSIP.cpp:86
OpenMS::IsotopeDistribution::ContainerType
std::vector< MassAbundance > ContainerType
Definition: IsotopeDistribution.h:72
MetaProSIPReporting::plotFilteredSpectra
static void plotFilteredSpectra(const String &output_dir, const String &tmp_path, const String &file_suffix, const String &file_extension, const vector< SIPPeptide > &sip_peptides, Size debug_level=0, const QString &executable=QString("R"))
Definition: MetaProSIP.cpp:467
OpenMS::ElementDB::getInstance
static const ElementDB * getInstance()
MetaProSIPReporting::createQualityReport
static void createQualityReport(const String &tmp_path, const String &qc_output_directory, const String &file_suffix, const String &file_extension, const vector< vector< SIPPeptide > > &sip_peptide_cluster, Size n_heatmap_bins, double score_plot_y_axis_min, bool report_natural_peptides, const QString &executable=QString("R"))
Definition: MetaProSIP.cpp:766
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
ThresholdMower.h
OpenMS::Internal::DIntervalBase::maxPosition
PositionType const & maxPosition() const
Accessor to maximum position.
Definition: DIntervalBase.h:130
MetaProSIPReporting::createCSVReport
static void createCSVReport(vector< vector< SIPPeptide > > &sippeptide_cluster, ofstream &os, map< String, String > &proteinid_to_description)
Definition: MetaProSIP.cpp:809
MetaProSIPInterpolation
Definition: MetaProSIP.cpp:194
OpenMS::FeatureMap::getUnassignedPeptideIdentifications
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
OpenMS::NonNegativeLeastSquaresSolver::solve
static Int solve(const Matrix< double > &A, const Matrix< double > &b, Matrix< double > &x)
This is a wrapper for the external nnls library for the non-negative least square problem Ax=b,...
SIPPeptide::sequence
AASequence sequence
sequence of the peptide
Definition: MetaProSIP.cpp:110
MetaProSIPClustering::clusterSIPPeptides
static vector< vector< SIPPeptide > > clusterSIPPeptides(const vector< double > &centers, vector< SIPPeptide > &sip_peptides)
Definition: MetaProSIP.cpp:320
MetaProSIPInterpolation::getHighPoints
static vector< RateScorePair > getHighPoints(double threshold, const MapRateToScoreType &rate2score, bool debug=false)
< Determine score maxima from rate to score distribution using derivatives from spline interpolation
Definition: MetaProSIP.cpp:198
OpenMS::MissedCleavages::mc_result_
std::vector< std::map< UInt32, UInt32 > > mc_result_
container that stores results
Definition: MissedCleavages.h:92
MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange
static IsotopePatterns calculateIsotopePatternsFor13CRange(const AASequence &peptide, Size additional_isotopes=5)
Definition: MetaProSIP.cpp:1336
OpenMS::Element
Representation of an element.
Definition: Element.h:53
SIPPeptide::charge
Int charge
charge of the peptide feature
Definition: MetaProSIP.cpp:128
OpenMS::File::getTempDirectory
static String getTempDirectory()
The current OpenMS temporary data path (for temporary files)
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
SizeLess::operator()
bool operator()(const vector< SIPPeptide > &a, const vector< SIPPeptide > &b) const
Definition: MetaProSIP.cpp:167
OpenMS::PeptideHit::extractProteinAccessionsSet
std::set< String > extractProteinAccessionsSet() const
extracts the set of non-empty protein accessions from peptide evidences
MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange
static IsotopePatterns calculateIsotopePatternsFor15NRange(const AASequence &peptide, Size additional_isotopes=5)
Definition: MetaProSIP.cpp:1455
OpenMS::CoarseIsotopePatternGenerator
Isotope pattern generator for coarse isotope distributions.
Definition: CoarseIsotopePatternGenerator.h:96
OpenMS::String::trim
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
OpenMS::Math::median
static double median(IteratorType begin, IteratorType end, bool sorted=false)
Calculates the median of a range of values.
Definition: StatisticFunctions.h:151
OpenMS::CubicSpline2d::eval
double eval(double x) const
evaluates the spline at position x
OpenMS::MzMLFile::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
MassDecompositionAlgorithm.h