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OpenMS
2.4.0
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37 #include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h>
40 #include <boost/shared_ptr.hpp>
59 void getRT(std::vector<double>& rt)
const override;
61 void getIntensity(std::vector<double>& intens)
const override;
63 float getIntensity()
const override;
65 double getRT()
const override;
85 boost::shared_ptr<OpenSwath::IFeature> getFeature(std::string nativeID)
override;
87 boost::shared_ptr<OpenSwath::IFeature> getPrecursorFeature(std::string nativeID)
override;
89 std::vector<std::string> getNativeIDs()
const override;
91 std::vector<std::string> getPrecursorIDs()
const override;
93 float getIntensity()
const override;
95 double getRT()
const override;
97 size_t size()
const override;
99 std::map<std::string, boost::shared_ptr<MockFeature> >
m_features;
117 std::size_t size()
const override;
119 std::vector<std::string> getNativeIDs()
const override;
121 void getLibraryIntensities(std::vector<double>& intensities)
const override;
138 double getValueAtRT(
double )
override;
cubic spline interpolation as described in R.L. Burden, J.D. Faires, Numerical Analysis,...
Definition: CubicSpline2d.h:53
std::vector< MassAbundance > ContainerType
Definition: IsotopeDistribution.h:80
Int getCharge() const
returns the charge of the peptide
std::size_t m_size
Definition: MockObjects.h:123
Base class for TOPP applications.
Definition: TOPPBase.h:150
double correlation
correlation coefficient
Definition: MetaProSIP.cpp:98
ConstIterator end() const
Gives access to the underlying text buffer.
void addLine(const StringType &line)
Definition: TextFile.h:112
datastructure for reporting an incorporation event
Definition: MetaProSIP.cpp:94
std::vector< double > m_rt_vec
Definition: MockObjects.h:67
static double sum(IteratorType begin, IteratorType end)
Calculates the sum of a range of values.
Definition: StatisticFunctions.h:121
PeakSpectrum reconstruction
signal reconstruction (debugging)
Definition: MetaProSIP.cpp:147
void set(const ContainerType &distribution)
overwrites the container which holds the distribution using distribution
static double median(IteratorType begin, IteratorType end, bool sorted=false)
Calculates the median of a range of values.
Definition: StatisticFunctions.h:152
Forward iterator for an area of peaks in an experiment.
Definition: AreaIterator.h:57
static String random(UInt length)
returns a random string of the given length. It consists of [0-9a-zA-Z]
Definition: MetaProSIP.cpp:1930
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
void insertHit(const PeptideHit &hit)
Appends a peptide hit.
double m_rt
Definition: MockObjects.h:102
Definition: MRMScoring.h:50
Representation of an element.
Definition: Element.h:53
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
String & substitute(char from, char to)
Replaces all occurrences of the character from by the character to.
This class serves for reading in and writing FASTA files.
Definition: FASTAFile.h:64
ConstAreaIterator areaEndConst() const
Returns an non-mutable invalid area iterator marking the end of an area.
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:119
A 2-dimensional raw data point or peak.
Definition: Peak2D.h:54
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
IsotopeDistribution estimateFromPeptideWeight(double average_weight)
Estimate Peptide Isotopedistribution from weight and number of isotopes that should be reported.
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:57
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
Mock object implementing ITransitionGroup.
Definition: MockObjects.h:108
const Element * getElement(const String &name) const
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
#define LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:446
Isotope pattern generator for coarse isotope distributions.
Definition: CoarseIsotopePatternGenerator.h:88
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
double getMonoWeight(Residue::ResidueType type=Residue::Full, Int charge=0) const
with N-terminus and C-terminus
Definition: Residue.h:152
double ratio
Recent ratio of numbers, see TOLERANCE_RELATIVE.
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
Definition: MetaProSIP.cpp:163
MapRateToScoreType correlation_map
Definition: MetaProSIP.cpp:137
MapRateToScoreType decomposition_map
Definition: MetaProSIP.cpp:135
double mass_theo
uncharged theoretical mass
Definition: MetaProSIP.cpp:117
double feature_rt
measurement time of feature apex [s]
Definition: MetaProSIP.cpp:121
std::map< std::string, boost::shared_ptr< MockFeature > > m_precursor_features
Definition: MockObjects.h:100
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:110
const ContainerType & getContainer() const
returns the container which holds the distribution
String toString() const
returns the peptide as string with modifications embedded in brackets
bool operator()(const vector< SIPPeptide > &a, const vector< SIPPeptide > &b) const
Definition: MetaProSIP.cpp:166
vector< String > accessions
protein accessions of the peptide
Definition: MetaProSIP.cpp:111
String toUnmodifiedString() const
returns the peptide as string without any modifications
Base::const_iterator const_iterator
Definition: MSExperiment.h:125
std::vector< double > m_intensity_vec
Definition: MockObjects.h:68
CoordinateType getMaxRT() const
returns the maximal retention time value
const double PROTON_MASS_U
bool operator()(const pair< SIPPeptide, Size > &a, const pair< SIPPeptide, Size > &b) const
Definition: MetaProSIP.cpp:176
double abundance
abundance of isotopologue
Definition: MetaProSIP.cpp:100
void setIntensity(IntensityType intensity)
Non-mutable access to the data point intensity (height)
Definition: Peak2D.h:172
void setPeptideIdentifications(const std::vector< PeptideIdentification > &peptides)
sets the PeptideIdentification vector
Size size() const
Definition: MSExperiment.h:127
void setHits(const std::vector< PeptideHit > &hits)
Sets the peptide hits.
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
double derivatives(double x, unsigned order) const
evaluates derivative of spline at position x
datastructure for reporting a peptide with one or more incorporation rates comparator for vectors of ...
Definition: MetaProSIP.cpp:107
vector< double > reconstruction_monoistopic
signal reconstruction of natural peptide (at mono-isotopic peak)
Definition: MetaProSIP.cpp:149
double RR
R squared of NNLS fit.
Definition: MetaProSIP.cpp:139
PositionType const & maxPosition() const
Accessor to maximum position.
Definition: DIntervalBase.h:127
int Int
Signed integer type.
Definition: Types.h:102
void assignRanks()
Sorts the hits by score and assigns ranks according to the scores.
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
float m_intensity
Definition: MockObjects.h:101
void updateRanges() override
Updates minimum and maximum position/intensity.
static String number(double d, UInt n)
returns a string for d with exactly n decimal places
#define LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:458
ConstAreaIterator areaBeginConst(CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz) const
Returns a non-mutable area iterator for area.
double mz_theo
theoretical mz
Definition: MetaProSIP.cpp:115
Mock object implementing ISignalToNoise.
Definition: MockObjects.h:132
Mock object implementing IMRMFeature.
Definition: MockObjects.h:76
double m_rt
Definition: MockObjects.h:70
#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
void setIsotopeDistribution(const IsotopeDistribution &isotopes)
sets the isotope distribution of the element
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 rate
Definition: MetaProSIP.cpp:89
Stream class for writing to comma/tab/...-separated values files.
Definition: SVOutStream.h:54
String feature_type
used to distinguish features from FeatureFinder, or synthetised from ids or averagine ids in reportin...
Definition: MetaProSIP.cpp:143
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
double score
Definition: MetaProSIP.cpp:90
EmpiricalFormula getFormula(Residue::ResidueType type=Residue::Full, Int charge=0) const
returns the formula of the peptide
Definition: MetaProSIP.cpp:183
CoordinateType getMZ() const
Non-mutable access to m/z.
Definition: Peak1D.h:113
AASequence sequence
sequence of the peptide
Definition: MetaProSIP.cpp:109
Iterator MZEnd(CoordinateType mz)
Binary search for peak range end (returns the past-the-end iterator)
void setHigherScoreBetter(bool value)
sets the peptide score orientation
Iterator MZBegin(CoordinateType mz)
Binary search for peak range begin.
double global_LR
labeling ratio for the whole spectrum used to detect global drifts. 13C/(12C+13C) intensities....
Definition: MetaProSIP.cpp:131
bool operator()(const SIPIncorporation &a, const SIPIncorporation &b) const
Definition: MetaProSIP.cpp:186
Definition: MetaProSIP.cpp:87
void setMZ(CoordinateType coordinate)
Mutable access to the m/z coordinate (index 1)
Definition: Peak2D.h:202
void setParameters(const Param ¶m)
Sets the parameters.
std::vector< std::string > m_native_ids
Definition: MockObjects.h:124
void insert(const Peak1D::CoordinateType &mass, const Peak1D::IntensityType &intensity)
Definition: IsotopeDistribution.h:225
void setMSLevel(UInt ms_level)
Sets the MS level.
QString toQString() const
Conversion to Qt QString.
Definition: ITransition.h:45
Definition: MetaProSIP.cpp:173
void setCharge(Int charge)
sets the charge of the peptide
bool unique
if the peptide is unique and therefor identifies the protein umambigously
Definition: MetaProSIP.cpp:113
PeakSpectrum accumulated
Definition: MetaProSIP.cpp:151
Int charge
charge of the peptide feature
Definition: MetaProSIP.cpp:127
std::set< String > extractProteinAccessionsSet() const
extracts the set of non-empty protein accessions from peptide evidences
bool empty() const
Definition: MSExperiment.h:137
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
std::vector< double > m_library_intensities
Definition: MockObjects.h:125
double eval(double x) const
evaluates the spline at position x
String & toUpper()
Converts the string to uppercase.
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
void sortByPosition()
Lexicographically sorts the peaks by their position.
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
void setSequence(const AASequence &sequence)
sets the peptide sequence
static const ElementDB * getInstance()
returns a pointer to the singleton instance of the element db
Definition: ElementDB.h:77
double m_sn_value
Definition: MockObjects.h:140
float m_intensity
Definition: MockObjects.h:69
Size non_zero_decomposition_coefficients
decomposition coefficients significantly larger than 0
Definition: MetaProSIP.cpp:145
vector< SIPIncorporation > incorporations
Definition: MetaProSIP.cpp:153
std::map< std::string, boost::shared_ptr< MockFeature > > m_features
Definition: MockObjects.h:99
ConstIterator begin() const
Gives access to the underlying text buffer.
Definition: ITransition.h:68
A container for features.
Definition: FeatureMap.h:93
Definition: IsotopeDistribution.h:72
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
IsotopePatterns patterns
Definition: MetaProSIP.cpp:155
static void load(const String &filename, std::vector< FASTAEntry > &data)
loads a FASTA file given by 'filename' and stores the information in 'data'
void clear()
clears the distribution and resets max isotope to 0
An LC-MS feature.
Definition: Feature.h:70
void filterPeakMap(PeakMap &exp)
static double mean(IteratorType begin, IteratorType end)
Calculates the mean of a range of values.
Definition: StatisticFunctions.h:134
double score
search engine score or q-value if fdr filtering is applied
Definition: MetaProSIP.cpp:119
double rate
rate
Definition: MetaProSIP.cpp:96
double getScore() const
returns the PSM score
PositionType const & minPosition() const
Accessor to minimum position.
Definition: DIntervalBase.h:121
double feature_mz
mz of feature apex [s]
Definition: MetaProSIP.cpp:123
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
ThresholdMower removes all peaks below a threshold.
Definition: ThresholdMower.h:51
ExitCodes
Exit codes.
Definition: TOPPBase.h:155
void updateRanges() override
Updates minimum and maximum position/intensity.
void store(const String &filename)
Writes the data to a file.
Management and storage of parameters / INI files.
Definition: Param.h:74
static String getTempDirectory()
The current OpenMS temporary data path (for temporary files)
Mock object implementing IFeature.
Definition: MockObjects.h:50
double explained_TIC_fraction
fraction of the MS2 TIC that is explained by the maximum correlating decomposition weights
Definition: MetaProSIP.cpp:141
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
static bool checkRDependencies(String tmp_path, StringList package_names, const QString &executable=QString("R"))
Definition: MetaProSIP.cpp:1934
void clear(bool clear_meta_data)
Clears all data and meta data.
Representation of a peptide/protein sequence.
Definition: AASequence.h:107
Definition: ITransition.h:76
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
vector< RateScorePair > correlation_maxima
Definition: MetaProSIP.cpp:133
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
CoordinateType getRT() const
returns the retention time of the current scan
Definition: AreaIterator.h:198
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:103
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
std::vector< String >::const_iterator ConstIterator
Non-mutable iterator.
Definition: TextFile.h:56
IntensityType getIntensity() const
Definition: Peak1D.h:108
ExitCodes main(int argc, const char **argv)
Main routine of all TOPP applications.
double mass_diff
Definition: MetaProSIP.cpp:129
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,...
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
ConstIterator RTBegin(CoordinateType rt) const
Fast search for spectrum range begin.
CoordinateType getMinRT() const
returns the minimal retention time value
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
Definition: ITransition.h:55
Representation of a peptide hit.
Definition: PeptideHit.h:54