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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";
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:72
Int getCharge() const
returns the charge of the peptide
Base class for TOPP applications.
Definition: TOPPBase.h:144
ConstIterator end() const
Gives access to the underlying text buffer.
void addLine(const StringType &line)
Definition: TextFile.h:112
static double sum(IteratorType begin, IteratorType end)
Calculates the sum of a range of values.
Definition: StatisticFunctions.h:120
void set(const ContainerType &distribution)
overwrites the container which holds the distribution using distribution
Storing a status of available/needed inputs (i.e. a set of Requires) as UInt64.
Definition: QCBase.h:118
static double median(IteratorType begin, IteratorType end, bool sorted=false)
Calculates the median of a range of values.
Definition: StatisticFunctions.h:151
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:1931
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
void insertHit(const PeptideHit &hit)
Appends a peptide hit.
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.
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:121
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:58
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
const Element * getElement(const String &name) const
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
Isotope pattern generator for coarse isotope distributions.
Definition: CoarseIsotopePatternGenerator.h:96
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.
Definition: MetaProSIP.cpp:164
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:112
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:167
String toUnmodifiedString() const
returns the peptide as string without any modifications or (e.g., "PEPTIDER")
Base::const_iterator const_iterator
Definition: MSExperiment.h:125
CoordinateType getMaxRT() const
returns the maximal retention time value
const double PROTON_MASS_U
#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
bool operator()(const pair< SIPPeptide, Size > &a, const pair< SIPPeptide, Size > &b) const
Definition: MetaProSIP.cpp:177
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
PositionType const & maxPosition() const
Accessor to maximum position.
Definition: DIntervalBase.h:130
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
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
ConstAreaIterator areaBeginConst(CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz) const
Returns a non-mutable area iterator for area.
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...
Stream class for writing to comma/tab/...-separated values files.
Definition: SVOutStream.h:54
This class serves as an abstract base class for all QC classes.
Definition: QCBase.h:52
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
EmpiricalFormula getFormula(Residue::ResidueType type=Residue::Full, Int charge=0) const
returns the formula of the peptide
Definition: MetaProSIP.cpp:184
CoordinateType getMZ() const
Non-mutable access to m/z.
Definition: Peak1D.h:115
Iterator MZEnd(CoordinateType mz)
Binary search for peak range end (returns the past-the-end iterator)
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
void setHigherScoreBetter(bool value)
sets the peptide score orientation
Iterator MZBegin(CoordinateType mz)
Binary search for peak range begin.
std::vector< std::map< UInt32, UInt32 > > mc_result_
container that stores results
Definition: MissedCleavages.h:92
bool operator()(const SIPIncorporation &a, const SIPIncorporation &b) const
Definition: MetaProSIP.cpp:187
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.
void insert(const Peak1D::CoordinateType &mass, const Peak1D::IntensityType &intensity)
Definition: IsotopeDistribution.h:214
void setMSLevel(UInt ms_level)
Sets the MS level.
QString toQString() const
Conversion to Qt QString.
Definition: MetaProSIP.cpp:174
void setCharge(Int charge)
sets the charge of the peptide
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
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:70
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()
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
ConstIterator begin() const
Gives access to the underlying text buffer.
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
A container for features.
Definition: FeatureMap.h:95
Definition: IsotopeDistribution.h:64
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
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
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:133
double getScore() const
returns the PSM score
PositionType const & minPosition() const
Accessor to minimum position.
Definition: DIntervalBase.h:124
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
ThresholdMower removes all peaks below a threshold.
Definition: ThresholdMower.h:51
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:73
static String getTempDirectory()
The current OpenMS temporary data path (for temporary files)
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
void clear(bool clear_meta_data)
Clears all data and meta data.
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
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
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
static bool checkRDependencies(const String &tmp_path, StringList package_names, const QString &executable=QString("R"))
Definition: MetaProSIP.cpp:1935
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:104
This class is a metric for the QualityControl TOPP Tool.
Definition: MissedCleavages.h:55
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
std::vector< String >::const_iterator ConstIterator
Non-mutable iterator.
Definition: TextFile.h:56
IntensityType getIntensity() const
Definition: Peak1D.h:110
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:505
Representation of a peptide hit.
Definition: PeptideHit.h:54