OpenMS  3.0.0
MultiplexSatelliteCentroided.h
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31 // $Maintainer: Lars Nilse $
32 // $Authors: Lars Nilse $
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34 
35 #pragma once
36 
38 
39 #include <map>
40 #include <vector>
41 #include <algorithm>
42 #include <iostream>
43 
44 namespace OpenMS
45 {
54  class OPENMS_DLLAPI MultiplexSatelliteCentroided
55  {
56  public:
57 
61  MultiplexSatelliteCentroided(size_t rt_idx, size_t mz_idx);
62 
66  size_t getMZidx() const;
67 
71  size_t getRTidx() const;
72 
73  private:
74 
80  size_t rt_idx_;
81  size_t mz_idx_;
82 
83  };
84 
85 }
86 
ConsensusXMLFile.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::ConsensusMap::applyMemberFunction
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all consensus features....
Definition: ConsensusMap.h:333
OpenMS::ConsensusXMLFile::store
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
OpenMS::Param::setValue
void setValue(const std::string &key, const ParamValue &value, const std::string &description="", const std::vector< std::string > &tags=std::vector< std::string >())
Sets a value.
OpenMS::MultiplexSatelliteCentroided::rt_idx_
size_t rt_idx_
indices of the satellite peak position in the centroided experiment
Definition: MultiplexSatelliteCentroided.h:80
OpenMS::Exception::InvalidSize
Invalid UInt exception.
Definition: Exception.h:295
OpenMS::Exception::InvalidValue
Invalid value exception.
Definition: Exception.h:327
OpenMS::MultiplexDeltaMasses::LabelSet
std::multiset< String > LabelSet
set of labels associated with a mass shift
Definition: MultiplexDeltaMasses.h:72
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
MzMLFile.h
ConsensusMap.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::ConsensusFeature::HandleSetType
std::set< FeatureHandle, FeatureHandle::IndexLess > HandleSetType
Type definitions.
Definition: ConsensusFeature.h:75
OpenMS::Peak2D::getIntensity
IntensityType getIntensity() const
Definition: Peak2D.h:166
Constants.h
OpenMS::BaseFeature::getPeptideIdentifications
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
OpenMS::Peak2D::setIntensity
void setIntensity(IntensityType intensity)
Sets data point intensity (height)
Definition: Peak2D.h:172
MultiplexDeltaMassesGenerator.h
OpenMS::BaseFeature::setPeptideIdentifications
void setPeptideIdentifications(const std::vector< PeptideIdentification > &peptides)
sets the PeptideIdentification vector
OpenMS::FeatureHandle::setMapIndex
void setMapIndex(UInt64 i)
Set the map index.
OpenMS::MultiplexSatelliteCentroided
data structure storing a single satellite peak
Definition: MultiplexSatelliteCentroided.h:54
OpenMS::FeatureHandle::setCharge
void setCharge(ChargeType charge)
Sets the charge.
OpenMS::MultiplexDeltaMassesGenerator::printDeltaMassesList
void printDeltaMassesList(std::ostream &stream) const
write the list of all mass patterns
OpenMS::Param::ParamIterator
Forward const iterator for the Param class.
Definition: Param.h:193
OpenMS::BaseFeature::setQuality
void setQuality(QualityType q)
Set the overall quality.
OpenMS::Peak2D::setRT
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
PeptideHit.h
OpenMS::MultiplexSatelliteCentroided::mz_idx_
size_t mz_idx_
Definition: MultiplexSatelliteCentroided.h:81
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...
OpenMS::Param::setMinInt
void setMinInt(const std::string &key, int min)
Sets the minimum value for the integer or integer list parameter key.
MultiplexIsotopicPeakPattern.h
OpenMS::BaseFeature::getCharge
const ChargeType & getCharge() const
Non-mutable access to charge state.
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OpenMS::ConsensusMap::ConstIterator
std::vector< ConsensusFeature >::const_iterator ConstIterator
Non-mutable iterator.
Definition: ConsensusMap.h:168
OpenMS::Peak2D::setMZ
void setMZ(CoordinateType coordinate)
Mutable access to the m/z coordinate (index 1)
Definition: Peak2D.h:202
OpenMS::DefaultParamHandler::getParameters
const Param & getParameters() const
Non-mutable access to the parameters.
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::Peak2D::getRT
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
OpenMS::ConsensusXMLFile::load
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
OpenMS::MultiplexDeltaMassesGenerator::printSamplesLabelsList
void printSamplesLabelsList(std::ostream &stream) const
write the list of labels for each of the sample
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
MultiplexDeltaMasses.h
MSExperiment.h
OpenMS::Param::setMinFloat
void setMinFloat(const std::string &key, double min)
Sets the minimum value for the floating point or floating point list parameter key.
OpenMS::ConsensusMap::getColumnHeaders
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
OpenMS::Param::end
ParamIterator end() const
End iterator for the internal tree.
OpenMS::Param::begin
ParamIterator begin() const
Begin iterator for the internal tree.
OpenMS::FeatureHandle
Representation of a Peak2D, RichPeak2D or Feature .
Definition: FeatureHandle.h:57
OpenMS::ConsensusFeature::size
Size size() const
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::MultiplexDeltaMassesGenerator::extractLabelSet
MultiplexDeltaMasses::LabelSet extractLabelSet(AASequence sequence)
extract the label set from the sequence
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::MSExperiment::ConstIterator
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:106
OpenMS::MultiplexDeltaMassesGenerator::getDeltaMassesList
std::vector< MultiplexDeltaMasses > getDeltaMassesList()
returns the list of mass shift patterns
OpenMS::Exception::MissingInformation
Not all required information provided.
Definition: Exception.h:186
OpenMS::Peak2D::getMZ
CoordinateType getMZ() const
Returns the m/z coordinate (index 1)
Definition: Peak2D.h:196
OpenMS::ConsensusFeature::getFeatures
const HandleSetType & getFeatures() const
Non-mutable access to the contained feature handles.
OpenMS::Constants::C13C12_MASSDIFF_U
const double C13C12_MASSDIFF_U
Definition: Constants.h:121
OpenMS::MSSpectrum::ConstIterator
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:130
OpenMS::MultiplexDeltaMassesGenerator
generates complete list of all possible mass shifts due to isotopic labelling
Definition: MultiplexDeltaMassesGenerator.h:60
PeptideIdentification.h
OpenMS::DIM_UNIT::RT
RT in seconds.
StandardTypes.h
OpenMS::BaseFeature::setCharge
void setCharge(const ChargeType &ch)
Set charge state.
OpenMS::BaseFeature::getQuality
QualityType getQuality() const
TOPPBase.h
OpenMS::ConsensusFeature::insert
void insert(const ConsensusFeature &cf)
Adds all feature handles (of the CF) into the consensus feature.
OpenMS::MSExperiment::RTEnd
ConstIterator RTEnd(CoordinateType rt) const
Fast search for spectrum range end (returns the past-the-end iterator)
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:58
OpenMS::MSExperiment::RTBegin
ConstIterator RTBegin(CoordinateType rt) const
Fast search for spectrum range begin.