public class PeakControllerImpl extends CachedDataAccessController
DataAccessController.ContentCategory, DataAccessController.Type
CHROMATOGRAM_TYPE, MZGRAPH_TYPE, SPECTRUM_TYPE
Constructor and Description |
---|
PeakControllerImpl(File file)
Construct a data access controller using a given mzML file
|
PeakControllerImpl(File file,
boolean useTitle) |
Modifier and Type | Method and Description |
---|---|
void |
close()
Close data access controller by resetting the data reader first
|
Chromatogram |
getChromatogramById(Comparable id,
boolean useCache)
Get chromatogram using a chromatogram id, gives the option to choose whether to use cache.
|
ExperimentMetaData |
getExperimentMetaData()
Get the Experiment Meta Data
|
IdentificationMetaData |
getIdentificationMetaData()
Get Identification Meta Data
|
MzGraphMetaData |
getMzGraphMetaData()
Get MzGraph Meta Data.
|
Spectrum |
getSpectrumById(Comparable id,
boolean useCache)
Get spectrum using a spectrum id, gives the option to choose whether to use cache.
|
Collection<Comparable> |
getSpectrumIds()
Get spectrum ids from cache
|
String |
getUid()
Get the unique id for this data access controller
It generates a MD5 hash using the absolute path of the file
This will guarantee the same id if the file path is the same
|
PeakUnmarshallerAdaptor |
getUnmarshaller()
Get the backend data reader
|
boolean |
hasMetaDataInformation()
The only file format that not contain any MetaData are the pure peak files.
|
static Class |
isValidFormat(File file)
Check a file is mzML file
|
getAvailablePeptideLevelScores, getAvailableProteinLevelScores, getCache, getCachingStrategy, getChromatogramById, getChromatogramIds, getMode, getNumberOfFragmentIons, getNumberOfPeptides, getNumberOfPTMs, getNumberOfPTMs, getNumberOfSpectrumPeaks, getNumberOfUniquePeptides, getPeptideByIndex, getPeptideByIndex, getPeptideIds, getPeptidePrecursorCharge, getPeptidePrecursorMz, getPeptideQuantUnit, getPeptidesBySpectrum, getPeptideScore, getPeptideSequence, getPeptideSequenceEnd, getPeptideSequences, getPeptideSequenceStart, getPeptideSpectrumId, getProteinAccession, getProteinAccessionVersion, getProteinAmbiguityGroupById, getProteinAmbiguityGroupIds, getProteinById, getProteinIds, getProteinQuantUnit, getProteinScore, getProteinThreshold, getPTMs, getSearchDatabase, getSearchDatabaseVersion, getSearchEngineCvTermReferences, getSpectraDataBasedOnTitle, getSpectrumById, getSpectrumIdForPeptide, getSpectrumMsLevel, getSpectrumPrecursorCharge, getSpectrumPrecursorIntensity, getSpectrumPrecursorMz, getSumOfIntensity, isSpectrumBasedOnTitle, populateCache, setCachingStrategy, setMode
getAdditional, getAvailableQuantPeptideLevelScores, getChromatogramByIndex, getChromatogramIndex, getContentCategories, getFragmentIons, getIsotopeLabellingQuantMethods, getLabelFreeQuantMethods, getName, getNumberOfChromatograms, getNumberOfIdentifiedSpectra, getNumberOfPeptides, getNumberOfPeptidesByRank, getNumberOfProteinAmbiguityGroups, getNumberOfProteins, getNumberOfQuantPeptides, getNumberOfQuantPeptides, getNumberOfQuantPTMs, getNumberOfQuantPTMs, getNumberOfReagents, getNumberOfSpectra, getNumberOfSubstitutionPTMs, getNumberOfSubstitutionPTMs, getNumberOfUniqueQuantPeptides, getPeptideEvidences, getPeptideIsotopeLabellingQuantMethods, getPeptideLabelFreeQuantMethods, getPeptideQuantData, getPeptideQuantStudyData, getPeptideRank, getPeptideTheoreticalMz, getProteinByIndex, getProteinCoverage, getProteinIsotopeLabellingQuantMethods, getProteinLabelFreeQuantMethods, getProteinQuantData, getProteinQuantStudyData, getProteinScores, getProteinSequence, getQuantMethods, getQuantPeptideByIndex, getQuantPeptideEvidences, getQuantPeptideIds, getQuantPeptideQuantScore, getQuantPeptideScore, getQuantPeptideSequence, getQuantPeptideSequences, getQuantPeptideSpectrumId, getQuantPTMs, getQuantSample, getReferenceSubSampleIndex, getSamples, getSource, getSpectraByIndex, getSpectrumIndex, getStudyVariables, getSubstitutionPTMs, getType, hasChromatogram, hasDecoyInformation, hasIsotopeLabellingQuantMethods, hasLabelFreeQuantMethods, hasPeptide, hasPeptideQuantData, hasPeptideTotalIntensities, hasProtein, hasProteinAmbiguityGroup, hasProteinQuantData, hasProteinSequence, hasProteinTotalIntensities, hasQuantData, hasQuantPeptide, hasSpectrum, indexOfProtein, isIdentifiedSpectrum, proteinsAreInferred, setContentCategories, setInferredProteinGroups, setName, setSource, setType, setUid
public PeakControllerImpl(File file)
file
- jmzReader fileDataAccessException
- data access exceptionpublic PeakControllerImpl(File file, boolean useTitle)
public PeakUnmarshallerAdaptor getUnmarshaller()
public String getUid()
getUid
in interface DataAccessController
getUid
in class AbstractDataAccessController
public Spectrum getSpectrumById(Comparable id, boolean useCache)
id
- spectrum iduseCache
- true means to use cachepublic Chromatogram getChromatogramById(Comparable id, boolean useCache)
getChromatogramById
in class CachedDataAccessController
id
- chromatogram iduseCache
- true means to use cachepublic void close()
close
in interface DataAccessController
close
in class CachedDataAccessController
public ExperimentMetaData getExperimentMetaData()
CachedDataAccessController
getExperimentMetaData
in interface MetaDataAccess
getExperimentMetaData
in class CachedDataAccessController
public MzGraphMetaData getMzGraphMetaData()
CachedDataAccessController
getMzGraphMetaData
in interface MetaDataAccess
getMzGraphMetaData
in class CachedDataAccessController
public IdentificationMetaData getIdentificationMetaData()
CachedDataAccessController
getIdentificationMetaData
in interface MetaDataAccess
getIdentificationMetaData
in class CachedDataAccessController
public static Class isValidFormat(File file)
file
- input filepublic boolean hasMetaDataInformation()
hasMetaDataInformation
in interface MetaDataAccess
hasMetaDataInformation
in class AbstractDataAccessController
public Collection<Comparable> getSpectrumIds()
CachedDataAccessController
getSpectrumIds
in interface MzGraphDataAccess
getSpectrumIds
in class CachedDataAccessController
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.