Modifier and Type | Method and Description |
---|---|
static int |
DataAccessUtilities.getMsLevel(Spectrum spectrum)
Get ms level of a spectrum
|
static int |
DataAccessUtilities.getNumberOfPeaks(Spectrum spectrum)
Count the number of peaks of a spectrum
|
static double |
DataAccessUtilities.getPrecursorIntensity(Spectrum spectrum)
Get precursor intensity
|
static double |
DataAccessUtilities.getPrecursorMz(Spectrum spectrum)
Get precursor m/z value
|
static double |
DataAccessUtilities.getSumOfIntensity(Spectrum spectrum)
Get the sum of all the peak intensities within a spectrum
|
static boolean |
DataAccessUtilities.hasFragmentIon(Spectrum spectrum)
Check whether spectrum has fragment ion information
|
Modifier and Type | Method and Description |
---|---|
Spectrum |
MzGraphDataAccess.getSpectrumById(Comparable id)
Get a Spectrum object via an spectrum id
|
Modifier and Type | Method and Description |
---|---|
Collection<Spectrum> |
MzGraphDataAccess.getSpectraByIndex(int index,
int offset)
Get a collection of spectra by its index and offset.
|
Modifier and Type | Method and Description |
---|---|
Spectrum |
CachedDataAccessController.getSpectrumById(Comparable id)
Get spectrum object from cache
It uses cache by default
|
Spectrum |
ReferencedIdentificationController.getSpectrumById(Comparable id,
boolean useCache)
Get spectrum using a spectrumIdentification id, gives the option to choose whether to
use cache.
|
Spectrum |
PeakControllerImpl.getSpectrumById(Comparable id,
boolean useCache)
Get spectrum using a spectrum id, gives the option to choose whether to use cache.
|
Modifier and Type | Method and Description |
---|---|
Collection<Spectrum> |
AbstractDataAccessController.getSpectraByIndex(int index,
int offset) |
Modifier and Type | Method and Description |
---|---|
static Spectrum |
PrideXmlTransformer.transformSpectrum(uk.ac.ebi.pride.jaxb.model.Spectrum rawSpec)
Convert spectrum
Note: supDes, supDataArrayBinary are ignored.
|
static Spectrum |
PeakTransformer.transformSpectrum(uk.ac.ebi.pride.tools.jmzreader.model.Spectrum spectrum)
Convert spectrum
|
static Spectrum |
MzXmlTransformer.transformSpectrum(uk.ac.ebi.pride.tools.jmzreader.model.Spectrum spectrum)
Convert spectrum
|
static Spectrum |
MzMLTransformer.transformSpectrum(uk.ac.ebi.jmzml.model.mzml.Spectrum spectrum)
Convert spectrum
|
static Spectrum |
MzDataTransformer.transformSpectrum(uk.ac.ebi.pride.tools.jmzreader.model.Spectrum spectrum)
Convert spectrum
|
Modifier and Type | Method and Description |
---|---|
Spectrum |
SpectrumIdentification.getSpectrum() |
Spectrum |
Precursor.getSpectrum() |
Spectrum |
Peptide.getSpectrum() |
Modifier and Type | Method and Description |
---|---|
void |
SpectrumIdentification.setSpectrum(Spectrum spectrum) |
void |
Precursor.setSpectrum(Spectrum spectrum) |
void |
Peptide.setSpectrum(Spectrum spectrum) |
Constructor and Description |
---|
Precursor(Spectrum spectrum,
SourceFile sourceFile,
String externalSpectrumID,
ParamGroup isolationWindow,
List<ParamGroup> selectedIon,
ParamGroup activation)
Constructor
|
Spectrum(Spectrum spectrum) |
SpectrumIdentification(Comparable id,
String name,
int chargeState,
double experimentalMassToCharge,
double calculatedMassToCharge,
double calculatedPI,
PeptideSequence peptideSequence,
int rank,
boolean passThreshold,
MassTable massTable,
Sample sample,
List<PeptideEvidence> peptideEvidenceList,
List<FragmentIon> fragmentation,
Score score,
Spectrum spectrum,
SpectraData spectraData)
Spectrum Identification Item
|
SpectrumIdentification(ParamGroup params,
Comparable id,
String name,
int chargeState,
double experimentalMassToCharge,
double calculatedMassToCharge,
double calculatedPI,
PeptideSequence peptideSequence,
int rank,
boolean passThreshold,
MassTable massTable,
Sample sample,
List<PeptideEvidence> peptideEvidenceList,
List<FragmentIon> fragmentation,
Score score,
Spectrum spectrum,
SpectraData spectraData)
Spectrum Identification Item
|
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.