OpenMS
2.5.0
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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 | requires () const override |
const String & | getName () const override |
Returns the name of the metric. More... | |
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_ |
String | name_ |
Additional Inherited Members | |
Public Types inherited from QCBase | |
enum | Requires : UInt64 { FAIL, RAWMZML, POSTFDRFEAT, PREFDRFEAT, CONTAMINANTS, TRAFOALIGN, SIZE_OF_REQUIRES } |
Enum to encode a file type as a bit. More... | |
Static Public Member Functions inherited from QCBase | |
template<typename MAP , typename T > | |
static void | iterateFeatureMap (MAP &fmap, T lambda) |
function, which iterates through all PeptideIdentifications of a given FeatureMap and applies a given lambda function More... | |
Static Public Attributes inherited from QCBase | |
static const std::string | names_of_requires [] |
strings corresponding to enum Requires 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 | ||
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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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