OpenMS  2.5.0
PoseClusteringAffineSuperimposer.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Eva Lange, Clemens Groepl $
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34 
35 
36 #pragma once
37 
40 #include <OpenMS/KERNEL/Peak2D.h>
41 
42 namespace OpenMS
43 {
44 
66  class OPENMS_DLLAPI PoseClusteringAffineSuperimposer :
67  public BaseSuperimposer
68  {
69 public:
70 
73 
75 
77  {}
78 
98  void run(const ConsensusMap & map_model, const ConsensusMap & map_scene, TransformationDescription & transformation) override;
99 
101  virtual void run(const std::vector<Peak2D> & map_model, const std::vector<Peak2D> & map_scene, TransformationDescription & transformation);
102 
105  {
107  }
108 
110  static const String getProductName()
111  {
112  return "poseclustering_affine";
113  }
114 
115  };
116 } // namespace OpenMS
117 
OpenMS::SpectrumLookup::findByRT
Size findByRT(double rt) const
Look up spectrum by retention time (RT).
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:144
AScore.h
OpenMS::AScore::compute
PeptideHit compute(const PeptideHit &hit, PeakSpectrum &real_spectrum)
Computes the AScore and returns all computed phospho-sites. The saved sequences contain only phospho ...
OpenMS::MSExperiment::getSpectrum
MSSpectrum & getSpectrum(Size id)
returns a single spectrum
OpenMS::IdXMLFile::store
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.
OpenMS::MSSpectrum::findNearest
Size findNearest(CoordinateType mz) const
Binary search for the peak nearest to a specific m/z.
OpenMS::PeptideHit::getSequence
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
OpenMS::MSExperiment::sortSpectra
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
OpenMS::Peak1D::setMZ
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:121
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:58
MzMLFile.h
OpenMS::PoseClusteringAffineSuperimposer
A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transf...
Definition: PoseClusteringAffineSuperimposer.h:66
ConsensusMap.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::PeakFileOptions::addMSLevel
void addMSLevel(int level)
adds a desired MS level for peaks to load
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
IdXMLFile.h
OpenMS::AASequence::toString
String toString() const
returns the peptide as string with modifications embedded in brackets
SpectrumMetaDataLookup.h
OpenMS::Constants::PROTON_MASS_U
const double PROTON_MASS_U
OpenMS::String::hasSubstring
bool hasSubstring(const String &string) const
true if String contains the string, false otherwise
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS::AScore
Implementation of the Ascore For a given peptide sequence and its MS/MS spectrum it identifies the mo...
Definition: AScore.h:70
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Peak2D.h
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
OpenMS::MzMLFile::load
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...
int
OpenMS::SpectrumLookup
Helper class for looking up spectra based on different attributes.
Definition: SpectrumLookup.h:67
OpenMS::SpectrumLookup::readSpectra
void readSpectra(const SpectrumContainer &spectra, const String &scan_regexp=default_scan_regexp)
Read and index spectra for later look-up.
Definition: SpectrumLookup.h:103
OpenMS::Peak1D::getMZ
CoordinateType getMZ() const
Non-mutable access to m/z.
Definition: Peak1D.h:115
OPENMS_LOG_DEBUG
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
OpenMS::MSSpectrum::clear
void clear(bool clear_meta_data)
Clears all data and meta data.
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::DefaultParamHandler::getDefaults
const Param & getDefaults() const
Non-mutable access to the default parameters.
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::PoseClusteringAffineSuperimposer::~PoseClusteringAffineSuperimposer
~PoseClusteringAffineSuperimposer() override
Destructor.
Definition: PoseClusteringAffineSuperimposer.h:76
OpenMS::MSSpectrum::sortByPosition
void sortByPosition()
Lexicographically sorts the peaks by their position.
IDMapper.h
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
MSExperiment.h
OpenMS::Param::update
bool update(const Param &p_outdated, const bool add_unknown=false)
Rescue parameter values from p_outdated to current param.
OpenMS::OpenMS_Log_debug
Logger::LogStream OpenMS_Log_debug
Global static instance of a LogStream to capture messages classified as debug output....
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::MetaInfoInterface::metaValueExists
bool metaValueExists(const String &name) const
Returns whether an entry with the given name exists.
OpenMS::MSExperiment::getSpectra
const std::vector< MSSpectrum > & getSpectra() const
returns the spectrum list
OpenMS::PeptideHit::getScore
double getScore() const
returns the PSM score
OpenMS::BaseSuperimposer
The base class of all superimposer algorithms.
Definition: BaseSuperimposer.h:56
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::PeakFileOptions::clearMSLevels
void clearMSLevels()
clears the MS levels
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
BaseSuperimposer.h
OpenMS::PoseClusteringAffineSuperimposer::create
static BaseSuperimposer * create()
Returns an instance of this class.
Definition: PoseClusteringAffineSuperimposer.h:104
OpenMS::Constants::C13C12_MASSDIFF_U
const double C13C12_MASSDIFF_U
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:61
OpenMS::MzMLFile::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h
OpenMS::PoseClusteringAffineSuperimposer::getProductName
static const String getProductName()
Returns the name of this module.
Definition: PoseClusteringAffineSuperimposer.h:110
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54