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OpenMS
2.6.0
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101 virtual void run(
const std::vector<Peak2D> & map_model,
const std::vector<Peak2D> & map_scene,
TransformationDescription & transformation);
112 return "poseclustering_affine";
Size findByRT(double rt) const
Look up spectrum by retention time (RT).
Base class for TOPP applications.
Definition: TOPPBase.h:144
PeptideHit compute(const PeptideHit &hit, PeakSpectrum &real_spectrum)
Computes the AScore and returns all computed phospho-sites. The saved sequences contain only phospho ...
MSSpectrum & getSpectrum(Size id)
returns a single spectrum
void store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
Size findNearest(CoordinateType mz) const
Binary search for the peak nearest to a specific m/z.
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:121
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:59
A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transf...
Definition: PoseClusteringAffineSuperimposer.h:66
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
void addMSLevel(int level)
adds a desired MS level for peaks to load
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
String toString() const
returns the peptide as string with modifications embedded in brackets
const double PROTON_MASS_U
bool hasSubstring(const String &string) const
true if String contains the string, false otherwise
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
Implementation of the Ascore For a given peptide sequence and its MS/MS spectrum it identifies the mo...
Definition: AScore.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
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...
Helper class for looking up spectra based on different attributes.
Definition: SpectrumLookup.h:67
void readSpectra(const SpectrumContainer &spectra, const String &scan_regexp=default_scan_regexp)
Read and index spectra for later look-up.
Definition: SpectrumLookup.h:103
CoordinateType getMZ() const
Non-mutable access to m/z.
Definition: Peak1D.h:115
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
void clear(bool clear_meta_data)
Clears all data and meta data.
void setParameters(const Param ¶m)
Sets the parameters.
const Param & getDefaults() const
Non-mutable access to the default parameters.
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
A container for consensus elements.
Definition: ConsensusMap.h:80
~PoseClusteringAffineSuperimposer() override
Destructor.
Definition: PoseClusteringAffineSuperimposer.h:76
void sortByPosition()
Lexicographically sorts the peaks by their position.
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
bool update(const Param &p_outdated, const bool add_unknown=false)
Rescue parameter values from p_outdated to current param.
Logger::LogStream OpenMS_Log_debug
Global static instance of a LogStream to capture messages classified as debug output....
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
const std::vector< MSSpectrum > & getSpectra() const
returns the spectrum list
double getScore() const
returns the PSM score
The base class of all superimposer algorithms.
Definition: BaseSuperimposer.h:56
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
void clearMSLevels()
clears the MS levels
Management and storage of parameters / INI files.
Definition: Param.h:73
static BaseSuperimposer * create()
Returns an instance of this class.
Definition: PoseClusteringAffineSuperimposer.h:104
const double C13C12_MASSDIFF_U
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
static const String getProductName()
Returns the name of this module.
Definition: PoseClusteringAffineSuperimposer.h:110
Used to load and store idXML files.
Definition: IdXMLFile.h:63
Representation of a peptide hit.
Definition: PeptideHit.h:55