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OpenMS
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QC metric calculating (un)calibrated m/z error. More...
#include <OpenMS/QC/MzCalibration.h>
Public Member Functions | |
| MzCalibration () | |
| Constructor. More... | |
| virtual | ~MzCalibration ()=default |
| Destructor. More... | |
| void | compute (FeatureMap &features, const MSExperiment &exp, const QCBase::SpectraMap &map_to_spectrum) |
| Writes results as meta values to the PeptideIdentification of the given FeatureMap. More... | |
| Status | requirements () const override |
| const String & | getName () const override |
| Returns the name of the metric. More... | |
 Public Member Functions inherited from QCBase | |
| bool | isRunnable (const Status &s) const |
Private Member Functions | |
| void | addMzMetaValues_ (PeptideIdentification &peptide_ID, const MSExperiment &exp, const QCBase::SpectraMap &map_to_spectrum) |
| calculate the m/z values and m/z errors and add them to the PeptideIdentification More... | |
Private Attributes | |
| double | mz_raw_ |
| double | mz_ref_ |
| bool | no_mzml_ |
Additional Inherited Members | |
| Public Types inherited from QCBase | |
| enum class | Requires : UInt64 { NOTHING , RAWMZML , POSTFDRFEAT , PREFDRFEAT , CONTAMINANTS , TRAFOALIGN , ID , SIZE_OF_REQUIRES } |
| Enum to encode a file type as a bit. More... | |
| enum class | ToleranceUnit { AUTO , PPM , DA , SIZE_OF_TOLERANCEUNIT } |
| using | Status = FlagSet< Requires > |
| Static Public Member Functions inherited from QCBase | |
| static bool | isLabeledExperiment (const ConsensusMap &cm) |
| check if the IsobaricAnalyzer TOPP tool was used to create this ConsensusMap More... | |
| template<typename MAP > | |
| static bool | hasPepID (const MAP &fmap) |
| does the container have a PeptideIdentification in its members or as unassignedPepID ? More... | |
| Static Public Attributes inherited from QCBase | |
| static const std::string | names_of_requires [] |
| strings corresponding to enum Requires More... | |
| static const std::string | names_of_toleranceUnit [] |
| strings corresponding to enum ToleranceUnit More... | |
QC metric calculating (un)calibrated m/z error.
The metric sets m/z-values of the original experiment and the calculated reference m/z-values, uncalibrated m/z error (ppm) and calibrated m/z error (ppm) as metavalues of all PeptideIdentifications in a FeatureMap.
For full functionality a PeakMap/MSExperiment with original m/z-values before m/z calibration generated by InternalCalibration has to be given. It's also possible to use this without an MzML File, but then only uncalibrated m/z error (ppm) will be reported. A FeatureMap after FDR is always required.
| MzCalibration | ( | ) |
Constructor.
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virtualdefault |
Destructor.
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private |
calculate the m/z values and m/z errors and add them to the PeptideIdentification
| void compute | ( | FeatureMap & | features, |
| const MSExperiment & | exp, | ||
| const QCBase::SpectraMap & | map_to_spectrum | ||
| ) |
Writes results as meta values to the PeptideIdentification of the given FeatureMap.
| features | FeatureMap with m/z-values of PeptideIdentification after calibration, meta values are added here |
| exp | PeakMap of the original experiment. Can be empty (i.e. not available). |
| map_to_spectrum | Map to find index of spectrum given by meta value at PepID |
| Exception::InvalidParameter | PeptideID is missing meta value 'spectrum_reference' |
| Exception::IllegalArgument | Spectrum for a PepID has MSLevel of 1 |
| Exception::MissingInformation | Meta value 'mz_raw' missing from MSExperiment |
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overridevirtual |
define the required input files only FeatureXML after FDR is ultimately necessary
Implements QCBase.
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private |
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private |
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private |
1.9.1 
