public class PrideXmlControllerImpl extends CachedDataAccessController
DataAccessController.ContentCategory, DataAccessController.Type
CHROMATOGRAM_TYPE, MZGRAPH_TYPE, SPECTRUM_TYPE
Constructor and Description |
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PrideXmlControllerImpl(File file) |
Modifier and Type | Method and Description |
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void |
close()
Close data access controller by clearing the cache first
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ParamGroup |
getAdditional()
Get additional parameters
|
List<CVLookup> |
getCvLookups()
Get a list of cv lookup objects.
|
List<DataProcessing> |
getDataProcessings()
Get a list of data processing objects
|
ExperimentMetaData |
getExperimentMetaData()
Get meta data related to this experiment
|
IdentificationMetaData |
getIdentificationMetaData()
Get Identification Meta Data
|
List<InstrumentConfiguration> |
getInstrumentConfigurations()
Get a list of instruments
|
MzGraphMetaData |
getMzGraphMetaData()
Get MzGraph Meta Data.
|
int |
getNumberOfPeptides()
Get the number of peptides.
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int |
getNumberOfPeptidesByRank(int rank)
Get the number of peptides by Rank, in PRIDE XML all peptides are rank 1.
|
List<Organization> |
getOrganizationContacts() |
Peptide |
getPeptideByIndex(Comparable proteinId,
Comparable index,
boolean useCache)
Get peptide using a given identification id and a given peptide index
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List<Person> |
getPersonContacts() |
Protein |
getProteinById(Comparable proteinId,
boolean useCache)
Get identification using a identification id, gives the option to choose whether to use cache.
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ExperimentProtocol |
getProtocol()
Get the protocol object
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uk.ac.ebi.pride.jaxb.xml.PrideXmlReader |
getReader()
Get the pride xml reader
|
List<Reference> |
getReferences()
Get a list of references
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List<Sample> |
getSamples()
Get a list of samples
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List<Software> |
getSoftwares()
Get a list of software
|
List<SourceFile> |
getSourceFiles()
Get a list of source files.
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String |
getUid()
Get md5 hash unique id
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protected void |
initialize() |
boolean |
isIdentifiedSpectrum(Comparable specId)
Check whether the spectrum has been identified.
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static boolean |
isValidFormat(File file)
Check a file is PRIDE XML file
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getAvailablePeptideLevelScores, getAvailableProteinLevelScores, getCache, getCachingStrategy, getChromatogramById, getChromatogramById, getChromatogramIds, getMode, getNumberOfFragmentIons, getNumberOfPeptides, getNumberOfPTMs, getNumberOfPTMs, getNumberOfSpectrumPeaks, getNumberOfUniquePeptides, 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, getSpectrumIds, getSpectrumMsLevel, getSpectrumPrecursorCharge, getSpectrumPrecursorIntensity, getSpectrumPrecursorMz, getSumOfIntensity, isSpectrumBasedOnTitle, populateCache, setCachingStrategy, setMode
getAvailableQuantPeptideLevelScores, getChromatogramByIndex, getChromatogramIndex, getContentCategories, getFragmentIons, getIsotopeLabellingQuantMethods, getLabelFreeQuantMethods, getName, getNumberOfChromatograms, getNumberOfIdentifiedSpectra, 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, getSource, getSpectraByIndex, getSpectrumIndex, getStudyVariables, getSubstitutionPTMs, getType, hasChromatogram, hasDecoyInformation, hasIsotopeLabellingQuantMethods, hasLabelFreeQuantMethods, hasMetaDataInformation, hasPeptide, hasPeptideQuantData, hasPeptideTotalIntensities, hasProtein, hasProteinAmbiguityGroup, hasProteinQuantData, hasProteinSequence, hasProteinTotalIntensities, hasQuantData, hasQuantPeptide, hasSpectrum, indexOfProtein, proteinsAreInferred, setContentCategories, setInferredProteinGroups, setName, setSource, setType, setUid
public PrideXmlControllerImpl(File file)
protected void initialize()
public uk.ac.ebi.pride.jaxb.xml.PrideXmlReader getReader()
public String getUid()
getUid
in interface DataAccessController
getUid
in class AbstractDataAccessController
public List<CVLookup> getCvLookups()
public List<SourceFile> getSourceFiles()
DataAccessException
public List<Organization> getOrganizationContacts()
public List<Sample> getSamples()
getSamples
in class AbstractDataAccessController
public List<Software> getSoftwares()
public List<InstrumentConfiguration> getInstrumentConfigurations()
public List<DataProcessing> getDataProcessings()
public List<Reference> getReferences()
public ExperimentProtocol getProtocol()
public ParamGroup getAdditional()
getAdditional
in class AbstractDataAccessController
public ExperimentMetaData getExperimentMetaData()
getExperimentMetaData
in interface MetaDataAccess
getExperimentMetaData
in class CachedDataAccessController
public IdentificationMetaData getIdentificationMetaData()
CachedDataAccessController
getIdentificationMetaData
in interface MetaDataAccess
getIdentificationMetaData
in class CachedDataAccessController
public MzGraphMetaData getMzGraphMetaData()
CachedDataAccessController
getMzGraphMetaData
in interface MetaDataAccess
getMzGraphMetaData
in class CachedDataAccessController
public boolean isIdentifiedSpectrum(Comparable specId)
isIdentifiedSpectrum
in interface MzGraphDataAccess
isIdentifiedSpectrum
in class AbstractDataAccessController
specId
- spectrum idpublic Protein getProteinById(Comparable proteinId, boolean useCache)
proteinId
- identification iduseCache
- true means to use cachepublic Peptide getPeptideByIndex(Comparable proteinId, Comparable index, boolean useCache)
getPeptideByIndex
in class CachedDataAccessController
proteinId
- identification idindex
- peptide indexuseCache
- whether to use cachepublic int getNumberOfPeptides()
getNumberOfPeptides
in interface PeptideDataAccess
getNumberOfPeptides
in class AbstractDataAccessController
public int getNumberOfPeptidesByRank(int rank)
getNumberOfPeptidesByRank
in interface PeptideDataAccess
getNumberOfPeptidesByRank
in class AbstractDataAccessController
public void close()
CachedDataAccessController
close
in interface DataAccessController
close
in class CachedDataAccessController
public static boolean isValidFormat(File file)
file
- input fileCopyright © 2015 European Bioinformatics Institute. All Rights Reserved.