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