OpenMS  2.4.0
MockObjects.h
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31 // $Maintainer: Hannes Roest $
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34 
35 #pragma once
36 
37 #include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h>
39 
40 #include <boost/shared_ptr.hpp>
41 #include <map>
42 #include <vector>
43 
44 namespace OpenSwath
45 {
46 
50  class OPENSWATHALGO_DLLAPI MockFeature :
51  public OpenSwath::IFeature
52  {
53 public:
54 
55  MockFeature();
56 
57  ~MockFeature() override;
58 
59  void getRT(std::vector<double>& rt) const override;
60 
61  void getIntensity(std::vector<double>& intens) const override;
62 
63  float getIntensity() const override;
64 
65  double getRT() const override;
66 
67  std::vector<double> m_rt_vec;
68  std::vector<double> m_intensity_vec;
69  float m_intensity;
70  double m_rt;
71  };
72 
76  class OPENSWATHALGO_DLLAPI MockMRMFeature :
78  {
79 public:
80 
82 
83  ~MockMRMFeature() override;
84 
85  boost::shared_ptr<OpenSwath::IFeature> getFeature(std::string nativeID) override;
86 
87  boost::shared_ptr<OpenSwath::IFeature> getPrecursorFeature(std::string nativeID) override;
88 
89  std::vector<std::string> getNativeIDs() const override;
90 
91  std::vector<std::string> getPrecursorIDs() const override;
92 
93  float getIntensity() const override;
94 
95  double getRT() const override;
96 
97  size_t size() const override;
98 
99  std::map<std::string, boost::shared_ptr<MockFeature> > m_features;
100  std::map<std::string, boost::shared_ptr<MockFeature> > m_precursor_features;
101  float m_intensity;
102  double m_rt;
103  };
104 
108  class OPENSWATHALGO_DLLAPI MockTransitionGroup :
110  {
111 public:
112 
114 
115  ~MockTransitionGroup() override;
116 
117  std::size_t size() const override;
118 
119  std::vector<std::string> getNativeIDs() const override;
120 
121  void getLibraryIntensities(std::vector<double>& intensities) const override;
122 
123  std::size_t m_size;
124  std::vector<std::string> m_native_ids;
125  std::vector<double> m_library_intensities;
126  };
127 
128 
132  class OPENSWATHALGO_DLLAPI MockSignalToNoise :
134  {
135 public:
137 
138  double getValueAtRT(double /* RT */) override;
139 
140  double m_sn_value;
141  };
142 
143 } //end namespace OpenMS
144 
OpenMS::EmpiricalFormula::getNumberOf
SignedSize getNumberOf(const Element *element) const
returns the number of atoms for a certain element (can be negative)
OpenMS::CubicSpline2d
cubic spline interpolation as described in R.L. Burden, J.D. Faires, Numerical Analysis,...
Definition: CubicSpline2d.h:53
OpenMS::IsotopeDistribution::ContainerType
std::vector< MassAbundance > ContainerType
Definition: IsotopeDistribution.h:80
OpenMS::PeptideHit::getCharge
Int getCharge() const
returns the charge of the peptide
OpenSwath::MockTransitionGroup::m_size
std::size_t m_size
Definition: MockObjects.h:123
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:363
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:150
SIPIncorporation::correlation
double correlation
correlation coefficient
Definition: MetaProSIP.cpp:98
OpenMS::TextFile::end
ConstIterator end() const
Gives access to the underlying text buffer.
OpenMS::TextFile::addLine
void addLine(const StringType &line)
Definition: TextFile.h:112
TextFile.h
MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange
static IsotopePatterns calculateIsotopePatternsFor13CRange(const AASequence &peptide, Size additional_isotopes=5)
Definition: MetaProSIP.cpp:1335
SIPIncorporation
datastructure for reporting an incorporation event
Definition: MetaProSIP.cpp:94
OpenSwath::MockFeature::m_rt_vec
std::vector< double > m_rt_vec
Definition: MockObjects.h:67
OpenMS::Math::sum
static double sum(IteratorType begin, IteratorType end)
Calculates the sum of a range of values.
Definition: StatisticFunctions.h:121
SIPPeptide::reconstruction
PeakSpectrum reconstruction
signal reconstruction (debugging)
Definition: MetaProSIP.cpp:147
TOPPMetaProSIP::isotopicIntensitiesToSpectrum
PeakSpectrum isotopicIntensitiesToSpectrum(double mz_start, double mass_diff, Int charge, vector< double > isotopic_intensities)
> converts a vector of isotopic intensities to a peak spectrum starting at mz=mz_start with mass_diff...
Definition: MetaProSIP.cpp:2579
ITransition.h
OpenMS::IsotopeDistribution::set
void set(const ContainerType &distribution)
overwrites the container which holds the distribution using distribution
TOPPMetaProSIP::registerOptionsAndFlags_
void registerOptionsAndFlags_() override
Sets the valid command line options (with argument) and flags (without argument).
Definition: MetaProSIP.cpp:2037
MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange
static IsotopePatterns calculateIsotopePatternsFor2HRange(const AASequence &peptide, Size additional_isotopes=5)
Definition: MetaProSIP.cpp:1523
MapRateToScoreType
map< double, double > MapRateToScoreType
Definition: MetaProSIP.cpp:83
TOPPMetaProSIP::extractIsotopicIntensities
vector< double > extractIsotopicIntensities(Size element_count, double mass_diff, double mz_tolerance_ppm, double seed_rt, double seed_mz, double seed_charge, const PeakMap &peak_map)
Definition: MetaProSIP.cpp:2343
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::Internal::AreaIterator
Forward iterator for an area of peaks in an experiment.
Definition: AreaIterator.h:57
OpenMS::String::random
static String random(UInt length)
returns a random string of the given length. It consists of [0-9a-zA-Z]
RIntegration
Definition: MetaProSIP.cpp:1930
MetaProSIPReporting::createCSVReport
static void createCSVReport(vector< vector< SIPPeptide > > &sippeptide_cluster, ofstream &os, map< String, String > &proteinid_to_description)
Definition: MetaProSIP.cpp:808
OpenMS::PeptideHit::getSequence
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
IsotopePattern
pair< double, vector< double > > IsotopePattern
Definition: MetaProSIP.cpp:84
TOPPMetaProSIP::extractPeakSpectrum
PeakSpectrum extractPeakSpectrum(Size element_count, double mass_diff, double rt, double feature_hit_theoretical_mz, Int feature_hit_charge, const PeakMap &peak_map)
Definition: MetaProSIP.cpp:2325
OpenMS::PeptideIdentification::insertHit
void insertHit(const PeptideHit &hit)
Appends a peptide hit.
CubicSpline2d.h
OpenSwath::MockMRMFeature::m_rt
double m_rt
Definition: MockObjects.h:102
OpenSwath
Definition: MRMScoring.h:50
Int
OpenMS::Element
Representation of an element.
Definition: Element.h:53
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.
Definition: FASTAFile.h:64
OpenMS::MSExperiment::areaEndConst
ConstAreaIterator areaEndConst() const
Returns an non-mutable invalid area iterator marking the end of an area.
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:197
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:665
OpenMS::Peak1D::setMZ
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:119
OpenMS::Peak2D
A 2-dimensional raw data point or peak.
Definition: Peak2D.h:54
OpenMS::Constants::k
const double k
OpenMS::Param::setValue
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
OpenMS::String::NONE
Definition: String.h:80
OpenMS::CoarseIsotopePatternGenerator::estimateFromPeptideWeight
IsotopeDistribution estimateFromPeptideWeight(double average_weight)
Estimate Peptide Isotopedistribution from weight and number of isotopes that should be reported.
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:57
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::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenSwath::MockTransitionGroup
Mock object implementing ITransitionGroup.
Definition: MockObjects.h:108
OpenMS::ElementDB::getElement
const Element * getElement(const String &name) const
OpenMS::TextFile
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
LOG_ERROR
#define LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:446
OpenMS::CoarseIsotopePatternGenerator
Isotope pattern generator for coarse isotope distributions.
Definition: CoarseIsotopePatternGenerator.h:88
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
FeatureXMLFile.h
MetaProSIPDecomposition::calculateIsotopePatternsFor13CRangeOfAveraginePeptide
static IsotopePatterns calculateIsotopePatternsFor13CRangeOfAveraginePeptide(double mass)
Definition: MetaProSIP.cpp:1705
OpenMS::Residue::Full
with N-terminus and C-terminus
Definition: Residue.h:152
OpenMS::Internal::ClassTest::ratio
double ratio
Recent ratio of numbers, see TOLERANCE_RELATIVE.
LOG_INFO
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
SizeLess
Definition: MetaProSIP.cpp:163
SIPPeptide::correlation_map
MapRateToScoreType correlation_map
Definition: MetaProSIP.cpp:137
SIPPeptide::decomposition_map
MapRateToScoreType decomposition_map
Definition: MetaProSIP.cpp:135
StatisticFunctions.h
SIPPeptide::mass_theo
double mass_theo
uncharged theoretical mass
Definition: MetaProSIP.cpp:117
SIPPeptide::feature_rt
double feature_rt
measurement time of feature apex [s]
Definition: MetaProSIP.cpp:121
OpenSwath::MockMRMFeature::m_precursor_features
std::map< std::string, boost::shared_ptr< MockFeature > > m_precursor_features
Definition: MockObjects.h:100
OpenMS::Peak1D::setIntensity
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:110
OpenMS::IsotopeDistribution::getContainer
const ContainerType & getContainer() const
returns the container which holds the distribution
OpenMS::AASequence::toString
String toString() const
returns the peptide as string with modifications embedded in brackets
SizeLess::operator()
bool operator()(const vector< SIPPeptide > &a, const vector< SIPPeptide > &b) const
Definition: MetaProSIP.cpp:166
SIPPeptide::accessions
vector< String > accessions
protein accessions of the peptide
Definition: MetaProSIP.cpp:111
OpenMS::AASequence::toUnmodifiedString
String toUnmodifiedString() const
returns the peptide as string without any modifications
OpenMS::MSExperiment::const_iterator
Base::const_iterator const_iterator
Definition: MSExperiment.h:125
MetaProSIPXICExtraction
Definition: MetaProSIP.cpp:1820
OpenSwath::MockFeature::m_intensity_vec
std::vector< double > m_intensity_vec
Definition: MockObjects.h:68
OpenMS::MSExperiment::getMaxRT
CoordinateType getMaxRT() const
returns the maximal retention time value
OpenMS::Constants::PROTON_MASS_U
const double PROTON_MASS_U
TOPPMetaProSIP::calculateGlobalLR
double calculateGlobalLR(const vector< double > &isotopic_intensities)
> calculate the global labeling ration based on all but the first 4 peaks
Definition: MetaProSIP.cpp:2896
SequenceLess::operator()
bool operator()(const pair< SIPPeptide, Size > &a, const pair< SIPPeptide, Size > &b) const
Definition: MetaProSIP.cpp:176
Constants.h
MetaProSIPClustering::clusterSIPPeptides
static vector< vector< SIPPeptide > > clusterSIPPeptides(const vector< double > &centers, vector< SIPPeptide > &sip_peptides)
Definition: MetaProSIP.cpp:319
SIPIncorporation::abundance
double abundance
abundance of isotopologue
Definition: MetaProSIP.cpp:100
OpenMS::Peak2D::setIntensity
void setIntensity(IntensityType intensity)
Non-mutable access to the data point intensity (height)
Definition: Peak2D.h:172
MetaProSIPDecomposition::getNumberOfLabelingElements
static Size getNumberOfLabelingElements(String labeling_element, const AASequence &peptide)
Definition: MetaProSIP.cpp:1408
MassDecomposition.h
OpenMS::BaseFeature::setPeptideIdentifications
void setPeptideIdentifications(const std::vector< PeptideIdentification > &peptides)
sets the PeptideIdentification vector
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:127
TOPPMetaProSIP::findApexRT
vector< double > findApexRT(const FeatureMap::iterator feature_it, double hit_rt, const PeakMap &peak_map, Size n_scans)
Definition: MetaProSIP.cpp:2489
OpenMS::PeptideIdentification::setHits
void setHits(const std::vector< PeptideHit > &hits)
Sets the peptide hits.
TOPPMetaProSIP::UNIDENTIFIED_STRING
std::string UNIDENTIFIED_STRING
Definition: MetaProSIP.cpp:2036
OpenMS::PeptideIdentification::getHits
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
MetaProSIPDecomposition::calculateIsotopePatternsFor15NRangeOfAveraginePeptide
static IsotopePatterns calculateIsotopePatternsFor15NRangeOfAveraginePeptide(double mass)
Definition: MetaProSIP.cpp:1666
OpenMS::CubicSpline2d::derivatives
double derivatives(double x, unsigned order) const
evaluates derivative of spline at position x
SIPPeptide
datastructure for reporting a peptide with one or more incorporation rates comparator for vectors of ...
Definition: MetaProSIP.cpp:107
SIPPeptide::reconstruction_monoistopic
vector< double > reconstruction_monoistopic
signal reconstruction of natural peptide (at mono-isotopic peak)
Definition: MetaProSIP.cpp:149
SIPPeptide::RR
double RR
R squared of NNLS fit.
Definition: MetaProSIP.cpp:139
Element.h
OpenMS::Internal::DIntervalBase::maxPosition
PositionType const & maxPosition() const
Accessor to maximum position.
Definition: DIntervalBase.h:127
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS::PeptideIdentification::assignRanks
void assignRanks()
Sorts the hits by score and assigns ranks according to the scores.
OpenMS::Peak2D::setRT
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenSwath::MockMRMFeature::m_intensity
float m_intensity
Definition: MockObjects.h:101
OpenMS::FeatureMap::updateRanges
void updateRanges() override
Updates minimum and maximum position/intensity.
OpenMS::String::number
static String number(double d, UInt n)
returns a string for d with exactly n decimal places
LOG_DEBUG
#define LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:458
NonNegativeLeastSquaresSolver.h
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:466
TOPPMetaProSIP::filterIsotopicIntensities
void filterIsotopicIntensities(vector< double >::const_iterator &pattern_begin, vector< double >::const_iterator &pattern_end, vector< double >::const_iterator &intensities_begin, vector< double >::const_iterator &intensities_end, double TIC_threshold=0.99)
> filter intensity to remove noise or additional incorporation peaks that otherwise might interfere w...
Definition: MetaProSIP.cpp:2121
OpenMS::Matrix< double >
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.
SIPPeptide::mz_theo
double mz_theo
theoretical mz
Definition: MetaProSIP.cpp:115
OpenSwath::MockSignalToNoise
Mock object implementing ISignalToNoise.
Definition: MockObjects.h:132
OpenSwath::MockMRMFeature
Mock object implementing IMRMFeature.
Definition: MockObjects.h:76
OpenSwath::MockFeature::m_rt
double m_rt
Definition: MockObjects.h:70
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.
TOPPMetaProSIP::ADDITIONAL_ISOTOPES
Size ADDITIONAL_ISOTOPES
Definition: MetaProSIP.cpp:2033
OpenMS::Element::setIsotopeDistribution
void setIsotopeDistribution(const IsotopeDistribution &isotopes)
sets the isotope distribution of the element
TOPPMetaProSIP::UNASSIGNED_ID_STRING
std::string UNASSIGNED_ID_STRING
Definition: MetaProSIP.cpp:2035
MetaProSIPDecomposition::calculateIsotopePatternsFor18ORangeOfAveraginePeptide
static IsotopePatterns calculateIsotopePatternsFor18ORangeOfAveraginePeptide(double mass)
Definition: MetaProSIP.cpp:1779
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...
RateScorePair::rate
double rate
Definition: MetaProSIP.cpp:89
double
FASTAFile.h
OpenMS::SVOutStream
Stream class for writing to comma/tab/...-separated values files.
Definition: SVOutStream.h:54
MetaProSIPReporting
Definition: MetaProSIP.cpp:360
SIPPeptide::feature_type
String feature_type
used to distinguish features from FeatureFinder, or synthetised from ids or averagine ids in reportin...
Definition: MetaProSIP.cpp:143
MetaProSIPInterpolation
Definition: MetaProSIP.cpp:193
MassDecompositionAlgorithm.h
CoarseIsotopePatternGenerator.h
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:1890
QProcess
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
MetaProSIPClustering
Definition: MetaProSIP.cpp:264
RateScorePair::score
double score
Definition: MetaProSIP.cpp:90
Param.h
OpenMS::AASequence::getFormula
EmpiricalFormula getFormula(Residue::ResidueType type=Residue::Full, Int charge=0) const
returns the formula of the peptide
MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange
static IsotopePatterns calculateIsotopePatternsFor18ORange(const AASequence &peptide, Size additional_isotopes=5)
Definition: MetaProSIP.cpp:1594
RIALess
Definition: MetaProSIP.cpp:183
OpenMS::Peak1D::getMZ
CoordinateType getMZ() const
Non-mutable access to m/z.
Definition: Peak1D.h:113
IsotopePatterns
vector< IsotopePattern > IsotopePatterns
Definition: MetaProSIP.cpp:85
GaussModel.h
SIPPeptide::sequence
AASequence sequence
sequence of the peptide
Definition: MetaProSIP.cpp:109
OpenMS::MSSpectrum::MZEnd
Iterator MZEnd(CoordinateType mz)
Binary search for peak range end (returns the past-the-end iterator)
OpenMS::PeptideIdentification::setHigherScoreBetter
void setHigherScoreBetter(bool value)
sets the peptide score orientation
OpenMS::MSSpectrum::MZBegin
Iterator MZBegin(CoordinateType mz)
Binary search for peak range begin.
SIPPeptide::global_LR
double global_LR
labeling ratio for the whole spectrum used to detect global drifts. 13C/(12C+13C) intensities....
Definition: MetaProSIP.cpp:131
OpenMS::DBoundingBox< 2 >
RIALess::operator()
bool operator()(const SIPIncorporation &a, const SIPIncorporation &b) const
Definition: MetaProSIP.cpp:186
RateScorePair
Definition: MetaProSIP.cpp:87
OpenMS::Peak2D::setMZ
void setMZ(CoordinateType coordinate)
Mutable access to the m/z coordinate (index 1)
Definition: Peak2D.h:202
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:1101
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenSwath::MockTransitionGroup::m_native_ids
std::vector< std::string > m_native_ids
Definition: MockObjects.h:124
OpenMS::IsotopeDistribution::insert
void insert(const Peak1D::CoordinateType &mass, const Peak1D::IntensityType &intensity)
Definition: IsotopeDistribution.h:225
OpenMS::MSSpectrum::setMSLevel
void setMSLevel(UInt ms_level)
Sets the MS level.
MetaProSIPReporting::createQualityReport
static void createQualityReport(String tmp_path, String qc_output_directory, 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:765
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
TOPPMetaProSIP::extractIncorporationsAtHeighestDecompositionWeights
void extractIncorporationsAtHeighestDecompositionWeights(SIPPeptide &sip_peptide, const IsotopePatterns &patterns, double weight_merge_window=5.0, double min_corr_threshold=0.5, double min_low_RIA_threshold=-1, double min_decomposition_weight=10.0)
> Collect decomposition coefficients. Starting at the largest decomposition weights merge smaller wei...
Definition: MetaProSIP.cpp:2729
OpenSwath::IFeature
Definition: ITransition.h:45
SequenceLess
Definition: MetaProSIP.cpp:173
Normalizer.h
OpenMS::PeptideHit::setCharge
void setCharge(Int charge)
sets the charge of the peptide
SIPPeptide::unique
bool unique
if the peptide is unique and therefor identifies the protein umambigously
Definition: MetaProSIP.cpp:113
SIPPeptide::accumulated
PeakSpectrum accumulated
Definition: MetaProSIP.cpp:151
SIPPeptide::charge
Int charge
charge of the peptide feature
Definition: MetaProSIP.cpp:127
OpenMS::PeptideHit::extractProteinAccessionsSet
std::set< String > extractProteinAccessionsSet() const
extracts the set of non-empty protein accessions from peptide evidences
OpenMS::MSExperiment::empty
bool empty() const
Definition: MSExperiment.h:137
seqan::find
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
OpenSwath::MockTransitionGroup::m_library_intensities
std::vector< double > m_library_intensities
Definition: MockObjects.h:125
OpenMS::CubicSpline2d::eval
double eval(double x) const
evaluates the spline at position x
OpenMS::String::toUpper
String & toUpper()
Converts the string to uppercase.
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
OpenMS::FeatureMap::getUnassignedPeptideIdentifications
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
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::ElementDB::getInstance
static const ElementDB * getInstance()
returns a pointer to the singleton instance of the element db
Definition: ElementDB.h:77
OpenSwath::MockSignalToNoise::m_sn_value
double m_sn_value
Definition: MockObjects.h:140
ModificationsDB.h
OpenSwath::MockFeature::m_intensity
float m_intensity
Definition: MockObjects.h:69
SVOutStream.h
main
int main(int argc, const char **argv)
Definition: MetaProSIP.cpp:3632
SIPPeptide::non_zero_decomposition_coefficients
Size non_zero_decomposition_coefficients
decomposition coefficients significantly larger than 0
Definition: MetaProSIP.cpp:145
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...
TOPPMetaProSIP::getBestRateScorePair
void getBestRateScorePair(const MapRateToScoreType &map_rate_to_score, double &best_rate, double &best_score)
Definition: MetaProSIP.cpp:2312
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:1823
SIPPeptide::incorporations
vector< SIPIncorporation > incorporations
Definition: MetaProSIP.cpp:153
OpenSwath::MockMRMFeature::m_features
std::map< std::string, boost::shared_ptr< MockFeature > > m_features
Definition: MockObjects.h:99
OpenMS::TextFile::begin
ConstIterator begin() const
Gives access to the underlying text buffer.
OpenSwath::ITransitionGroup
Definition: ITransition.h:68
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:93
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:72
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
SIPPeptide::patterns
IsotopePatterns patterns
Definition: MetaProSIP.cpp:155
TOPPMetaProSIP::extractIncorporationsAtCorrelationMaxima
void extractIncorporationsAtCorrelationMaxima(SIPPeptide &sip_peptide, const IsotopePatterns &patterns, double weight_merge_window=5.0, double min_corr_threshold=0.5, double min_decomposition_weight=10.0)
Definition: MetaProSIP.cpp:2594
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'
OpenMS::IsotopeDistribution::clear
void clear()
clears the distribution and resets max isotope to 0
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::ThresholdMower::filterPeakMap
void filterPeakMap(PeakMap &exp)
OpenMS::Math::mean
static double mean(IteratorType begin, IteratorType end)
Calculates the mean of a range of values.
Definition: StatisticFunctions.h:134
SIPPeptide::score
double score
search engine score or q-value if fdr filtering is applied
Definition: MetaProSIP.cpp:119
SIPIncorporation::rate
double rate
rate
Definition: MetaProSIP.cpp:96
TOPPMetaProSIP::main_
ExitCodes main_(int, const char **) override
The actual "main" method. main_() is invoked by main().
Definition: MetaProSIP.cpp:2914
MetaProSIPDecomposition
Definition: MetaProSIP.cpp:1251
OpenMS::PeptideHit::getScore
double getScore() const
returns the PSM score
TOPPMetaProSIP::calculateCorrelation
void calculateCorrelation(Size n_element, const vector< double > &isotopic_intensities, IsotopePatterns patterns, MapRateToScoreType &map_rate_to_correlation_score, String labeling_element, double mass, double min_correlation_distance_to_averagine)
Returns highest scoring rate and score pair in the map.
Definition: MetaProSIP.cpp:2186
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:81
TOPPMetaProSIP::mergeSpectra
PeakSpectrum mergeSpectra(const PeakMap &to_merge)
Definition: MetaProSIP.cpp:2566
ElementDB.h
OpenMS::Internal::DIntervalBase::minPosition
PositionType const & minPosition() const
Accessor to minimum position.
Definition: DIntervalBase.h:121
SIPPeptide::feature_mz
double feature_mz
mz of feature apex [s]
Definition: MetaProSIP.cpp:123
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
OpenMS::ThresholdMower
ThresholdMower removes all peaks below a threshold.
Definition: ThresholdMower.h:51
OpenMS::TOPPBase::ExitCodes
ExitCodes
Exit codes.
Definition: TOPPBase.h:155
MetaProSIPClustering::getRIAClusterCenter
static vector< double > getRIAClusterCenter(const vector< SIPPeptide > &sip_peptides, bool debug=false)
Definition: MetaProSIP.cpp:267
OpenMS::MSExperiment::updateRanges
void updateRanges() override
Updates minimum and maximum position/intensity.
OpenMS::TextFile::store
void store(const String &filename)
Writes the data to a file.
TOPPMetaProSIP
Definition: MetaProSIP.cpp:2019
TOPPMetaProSIP::FEATURE_STRING
std::string FEATURE_STRING
Definition: MetaProSIP.cpp:2034
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:74
OpenMS::File::getTempDirectory
static String getTempDirectory()
The current OpenMS temporary data path (for temporary files)
OpenSwath::MockFeature
Mock object implementing IFeature.
Definition: MockObjects.h:50
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:141
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:458
RIntegration::checkRDependencies
static bool checkRDependencies(String tmp_path, StringList package_names, const QString &executable=QString("R"))
Definition: MetaProSIP.cpp:1934
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:107
OpenSwath::ISignalToNoise
Definition: ITransition.h:76
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:544
OpenMS::MSExperiment::ConstIterator
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
OpenMS::AASequence::fromString
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
SIPPeptide::correlation_maxima
vector< RateScorePair > correlation_maxima
Definition: MetaProSIP.cpp:133
TOPPMetaProSIP::writePeakIntensities_
void writePeakIntensities_(SVOutStream &out_stream, vector< double > isotopic_intensities, bool write_13Cpeaks)
Definition: MetaProSIP.cpp:2392
OpenMS::PeakFileOptions::setMSLevels
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
OpenMS::Internal::AreaIterator::getRT
CoordinateType getRT() const
returns the retention time of the current scan
Definition: AreaIterator.h:198
SpectrumAlignment.h
PeakPickerHiRes.h
OpenMS::MSSpectrum::ConstIterator
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:103
MetaProSIPDecomposition::calculateIsotopePatternsFor2HRangeOfAveraginePeptide
static IsotopePatterns calculateIsotopePatternsFor2HRangeOfAveraginePeptide(double mass)
Definition: MetaProSIP.cpp:1741
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
MetaProSIPXICExtraction::correlateXICsToMono
static vector< double > correlateXICsToMono(const vector< vector< double > > &xics)
Definition: MetaProSIP.cpp:1877
OpenMS::TextFile::ConstIterator
std::vector< String >::const_iterator ConstIterator
Non-mutable iterator.
Definition: TextFile.h:56
OpenMS::Peak1D::getIntensity
IntensityType getIntensity() const
Definition: Peak1D.h:108
OpenMS::TOPPBase::main
ExitCodes main(int argc, const char **argv)
Main routine of all TOPP applications.
StandardTypes.h
TOPPMetaProSIP::TOPPMetaProSIP
TOPPMetaProSIP()
Definition: MetaProSIP.cpp:2023
SIPPeptide::mass_diff
double mass_diff
Definition: MetaProSIP.cpp:129
File.h
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,...
OpenMS::MzMLFile::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
TOPPBase.h
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:1255
MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange
static IsotopePatterns calculateIsotopePatternsFor15NRange(const AASequence &peptide, Size additional_isotopes=5)
Definition: MetaProSIP.cpp:1454
TOPPMetaProSIP::normalizeToMax
MapRateToScoreType normalizeToMax(const MapRateToScoreType &map_rate_to_decomposition_weight)
Definition: MetaProSIP.cpp:2457
ThresholdMower.h
OpenMS::MSExperiment::RTBegin
ConstIterator RTBegin(CoordinateType rt) const
Fast search for spectrum range begin.
OpenMS::MSExperiment::getMinRT
CoordinateType getMinRT() const
returns the minimal retention time value
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:1225
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:509
OpenSwath::IMRMFeature
Definition: ITransition.h:55
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54