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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]
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.
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
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
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
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
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.
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
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