public interface MzGraphDataAccess
Modifier and Type | Field and Description |
---|---|
static String |
CHROMATOGRAM_TYPE
fired when a chromatogram object has changed
|
static String |
MZGRAPH_TYPE
fired when a mz graph object has changed
|
static String |
SPECTRUM_TYPE
fired when a spectrum object has changed
|
Modifier and Type | Method and Description |
---|---|
Chromatogram |
getChromatogramById(Comparable chromaId)
Get a Chromatogram object
|
Collection<Chromatogram> |
getChromatogramByIndex(int index,
int offset)
Get a collection of chromatograms by its index and offset.
|
Collection<Comparable> |
getChromatogramIds()
Get a collection of chromatogram ids.
|
int |
getChromatogramIndex(Comparable chromaId)
Get the index of a chromatogram by its id
|
int |
getNumberOfChromatograms()
Get number of chromatograms
|
int |
getNumberOfIdentifiedSpectra()
Get the number of identified spectra.
|
int |
getNumberOfSpectra()
Get the number of spectra.
|
int |
getNumberOfSpectrumPeaks(Comparable specId)
Get the number peaks of a spectrum
|
List<Peptide> |
getPeptidesBySpectrum(Comparable specId)
Retrieve the Identified Peptides related with one spectrum
|
Collection<Spectrum> |
getSpectraByIndex(int index,
int offset)
Get a collection of spectra by its index and offset.
|
Spectrum |
getSpectrumById(Comparable id)
Get a Spectrum object via an spectrum id
|
Comparable |
getSpectrumIdForPeptide(Comparable psmID)
Convert the PSM id to spectrum ID
|
Collection<Comparable> |
getSpectrumIds()
Get a collection of spectrum ids
|
int |
getSpectrumIndex(Comparable id)
Get the index of a spectrum using its id
|
int |
getSpectrumMsLevel(Comparable specId)
Get the ms level of a spectrum.
|
Integer |
getSpectrumPrecursorCharge(Comparable specId)
Get the precursor charge of a spectrum.
|
double |
getSpectrumPrecursorIntensity(Comparable specId)
Get the precursor's intensity of a spectrum.
|
double |
getSpectrumPrecursorMz(Comparable specId)
Get the precursor's m/z value of a spectrum.
|
double |
getSumOfIntensity(Comparable specId)
Get the sum of intensity of a spectrum.
|
boolean |
hasChromatogram()
Whether this controller contains chromatogram.
|
boolean |
hasSpectrum()
Whether this controller contains spectra
|
boolean |
isIdentifiedSpectrum(Comparable specId)
Check whether the given spectrum is identified.
|
static final String CHROMATOGRAM_TYPE
static final String MZGRAPH_TYPE
static final String SPECTRUM_TYPE
boolean hasSpectrum()
boolean hasChromatogram()
int getNumberOfSpectra()
int getNumberOfIdentifiedSpectra()
Collection<Comparable> getSpectrumIds()
int getSpectrumIndex(Comparable id)
id
- spectrum idSpectrum getSpectrumById(Comparable id)
id
- Spectrum idCollection<Spectrum> getSpectraByIndex(int index, int offset)
index
- the start index of the spectrum.offset
- the max number of spectra to get.boolean isIdentifiedSpectrum(Comparable specId)
specId
- spectrum idList<Peptide> getPeptidesBySpectrum(Comparable specId)
specId
- Spectrum-Identification-Item IdentifierComparable getSpectrumIdForPeptide(Comparable psmID)
psmID
- Spectrum-Identification-Item Identifierint getNumberOfSpectrumPeaks(Comparable specId)
specId
- spectrum id.int getSpectrumMsLevel(Comparable specId)
specId
- spectrum id.Integer getSpectrumPrecursorCharge(Comparable specId)
specId
- spectrum id.double getSpectrumPrecursorMz(Comparable specId)
specId
- spectrum id.double getSpectrumPrecursorIntensity(Comparable specId) throws DataAccessException
specId
- spectrum id.DataAccessException
- data access exception.double getSumOfIntensity(Comparable specId) throws DataAccessException
specId
- spectrum id.DataAccessException
- data access exception.int getNumberOfChromatograms() throws DataAccessException
DataAccessException
- throw a exception when there is an error accessing the data source.Collection<Comparable> getChromatogramIds() throws DataAccessException
DataAccessException
- throw a exception when there is an error accessing the data sourceint getChromatogramIndex(Comparable chromaId) throws DataAccessException
chromaId
- chromatogram idDataAccessException
- data access exceptionChromatogram getChromatogramById(Comparable chromaId) throws DataAccessException
chromaId
- chromatogram string idDataAccessException
- throw a exception when there is an error accessing the data sourceCollection<Chromatogram> getChromatogramByIndex(int index, int offset) throws DataAccessException
index
- index of the starting chromatogram.offset
- the number of chromatogram to get.DataAccessException
- throw a exception when there is an error accessing the data source.Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.