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OpenMS
2.6.0
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66 size_t getMZidx()
const;
71 size_t getRTidx()
const;
Base class for TOPP applications.
Definition: TOPPBase.h:144
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all consensus features....
Definition: ConsensusMap.h:335
void setMinFloat(const String &key, double min)
Sets the minimum value for the floating point or floating point list parameter key.
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
size_t rt_idx_
indices of the satellite peak position in the centroided experiment
Definition: MultiplexSatelliteCentroided.h:80
Invalid UInt exception.
Definition: Exception.h:303
Invalid value exception.
Definition: Exception.h:335
std::multiset< String > LabelSet
set of labels associated with a mass shift
Definition: MultiplexDeltaMasses.h:73
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:59
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
std::set< FeatureHandle, FeatureHandle::IndexLess > HandleSetType
Type definitions.
Definition: ConsensusFeature.h:75
IntensityType getIntensity() const
Definition: Peak2D.h:166
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
returns a const reference to the PeptideIdentification vector
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
void setMapIndex(UInt64 i)
Set the map index.
data structure storing a single satellite peak
Definition: MultiplexSatelliteCentroided.h:54
void setCharge(ChargeType charge)
Sets the charge.
void printDeltaMassesList(std::ostream &stream) const
write the list of all mass patterns
Forward const iterator for the Param class.
Definition: Param.h:197
void setQuality(QualityType q)
Set the overall quality.
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
size_t mz_idx_
Definition: MultiplexSatelliteCentroided.h:81
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...
void setMinInt(const String &key, Int min)
Sets the minimum value for the integer or integer list parameter key.
const ChargeType & getCharge() const
Non-mutable access to charge state.
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
std::vector< ConsensusFeature >::const_iterator ConstIterator
Non-mutable iterator.
Definition: ConsensusMap.h:172
void setMZ(CoordinateType coordinate)
Mutable access to the m/z coordinate (index 1)
Definition: Peak2D.h:202
const Param & getParameters() const
Non-mutable access to the parameters.
A container for consensus elements.
Definition: ConsensusMap.h:80
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
void printSamplesLabelsList(std::ostream &stream) const
write the list of labels for each of the sample
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
ParamIterator end() const
End iterator for the internal tree.
ParamIterator begin() const
Begin iterator for the internal tree.
Representation of a Peak2D, RichPeak2D or Feature .
Definition: FeatureHandle.h:57
Management and storage of parameters / INI files.
Definition: Param.h:73
MultiplexDeltaMasses::LabelSet extractLabelSet(AASequence sequence)
extract the label set from the sequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
std::vector< MultiplexDeltaMasses > getDeltaMassesList()
returns the list of mass shift patterns
CoordinateType getMZ() const
Returns the m/z coordinate (index 1)
Definition: Peak2D.h:196
const HandleSetType & getFeatures() const
Non-mutable access to the contained feature handles.
const double C13C12_MASSDIFF_U
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:128
generates complete list of all possible mass shifts due to isotopic labelling
Definition: MultiplexDeltaMassesGenerator.h:60
void setCharge(const ChargeType &ch)
Set charge state.
QualityType getQuality() const
Non-mutable access to the overall quality.
void insert(const ConsensusFeature &cf)
Adds all feature handles (of the CF) into the consensus feature.
ConstIterator RTEnd(CoordinateType rt) const
Fast search for spectrum range end (returns the past-the-end iterator)
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:62
ConstIterator RTBegin(CoordinateType rt) const
Fast search for spectrum range begin.