public abstract class CachedDataAccessController extends AbstractDataAccessController
DataAccessController.ContentCategory, DataAccessController.Type
CHROMATOGRAM_TYPE, MZGRAPH_TYPE, SPECTRUM_TYPE
Constructor and Description |
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CachedDataAccessController() |
CachedDataAccessController(DataAccessMode mode) |
CachedDataAccessController(Object source,
DataAccessMode mode) |
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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List<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> |
getAvailablePeptideLevelScores()
This function return the possible peptide scores in the Source.
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List<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> |
getAvailableProteinLevelScores()
This function return the possible protein scores in the Source.
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Cache |
getCache() |
CachingStrategy |
getCachingStrategy() |
Chromatogram |
getChromatogramById(Comparable chromaId)
Get chromatogram object form cache
It uses cache by default
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Chromatogram |
getChromatogramById(Comparable id,
boolean useCache)
Get chromatogram using a chromatogram id, gives the option to choose whether to use cache.
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Collection<Comparable> |
getChromatogramIds()
Get chromatogram ids from cache
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ExperimentMetaData |
getExperimentMetaData()
Get the Experiment Meta Data
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IdentificationMetaData |
getIdentificationMetaData()
Get Identification Meta Data
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DataAccessMode |
getMode()
Get the runtime mode
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MzGraphMetaData |
getMzGraphMetaData()
Get MzGraph Meta Data.
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int |
getNumberOfFragmentIons(Comparable proteinId,
Comparable peptideId)
Get the number of fragment ions in a given peptide
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int |
getNumberOfPeptides(Comparable proteinId)
Get number of peptides using identification id.
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int |
getNumberOfPTMs(Comparable proteinId)
Get number of ptms using identification id.
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int |
getNumberOfPTMs(Comparable proteinId,
Comparable peptideId)
Get number of ptms using peptide id.
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int |
getNumberOfSpectrumPeaks(Comparable specId)
Get number of peaks using spectrum id.
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int |
getNumberOfUniquePeptides(Comparable proteinId)
Get number of unique peptides using identification id.
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Peptide |
getPeptideByIndex(Comparable proteinId,
Comparable index)
This is convenient method for accessing peptide.
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Peptide |
getPeptideByIndex(Comparable proteinId,
Comparable index,
boolean useCache) |
Collection<Comparable> |
getPeptideIds(Comparable proteinId)
Get peptide ids using identification id.
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Integer |
getPeptidePrecursorCharge(Comparable proteinId,
Comparable peptideId)
Get precursor charge on peptide level
Note: sometimes, precursor charge at the peptide level is different from the precursor charge at the spectrum level
As the peptide-level precursor charge is often assigned by search engine rather than ms instrument
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double |
getPeptidePrecursorMz(Comparable proteinId,
Comparable peptideId)
Get precursor m/z from the peptide level
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uk.ac.ebi.pride.utilities.term.QuantCvTermReference |
getPeptideQuantUnit()
Get peptide quantification unit
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List<Peptide> |
getPeptidesBySpectrum(Comparable specId)
Retrieve the Identified Peptides related with one spectrum
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Score |
getPeptideScore(Comparable proteinId,
Comparable peptideId)
Get peptide score from search engine
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String |
getPeptideSequence(Comparable proteinId,
Comparable peptideId)
Get peptide sequence using identification id and peptide id.
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int |
getPeptideSequenceEnd(Comparable proteinId,
Comparable peptideId)
Get peptide sequence stop using identification id and peptide id.
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List<String> |
getPeptideSequences(Comparable proteinId)
Get peptide sequences using identification id.
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int |
getPeptideSequenceStart(Comparable proteinId,
Comparable peptideId)
Get peptide sequence start using identification id and peptide id.
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Comparable |
getPeptideSpectrumId(Comparable proteinId,
Comparable peptideId)
Get peptide spectrum id using identification id and peptide id.
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String |
getProteinAccession(Comparable proteinId)
Get protein accession value using identification id.
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String |
getProteinAccessionVersion(Comparable proteinId)
Get protein accession version using identification id.
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ProteinGroup |
getProteinAmbiguityGroupById(Comparable proteinGroupId)
Get protein ambiguity group using protein group id
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Collection<Comparable> |
getProteinAmbiguityGroupIds()
Return a collection of the protein group identifiers
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Protein |
getProteinById(Comparable proteinId)
Get identification object from cache
It uses the cache by default
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Collection<Comparable> |
getProteinIds()
Get identification ids from cache
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uk.ac.ebi.pride.utilities.term.QuantCvTermReference |
getProteinQuantUnit()
Get protein quantification unit
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double |
getProteinScore(Comparable proteinId)
Get identification score using identification id.
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double |
getProteinThreshold(Comparable proteinId)
Get identification threshold using identification id.
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List<Modification> |
getPTMs(Comparable proteinId,
Comparable peptideId)
Get ptms using identification id nad peptide id
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SearchDataBase |
getSearchDatabase(Comparable proteinId)
Get search database using identification id
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String |
getSearchDatabaseVersion(Comparable proteinId)
Get search database version using identification id
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List<uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference> |
getSearchEngineCvTermReferences()
Get search engine type
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List<Comparable> |
getSpectraDataBasedOnTitle()
In some cases (WIFF files) the spectrum is referenced using the TITLE instead of using the index.
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Spectrum |
getSpectrumById(Comparable id)
Get spectrum object from cache
It uses cache by default
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Comparable |
getSpectrumIdForPeptide(Comparable psmID)
Convert PSM id to Spectrum ID
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Collection<Comparable> |
getSpectrumIds()
Get spectrum ids from cache
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int |
getSpectrumMsLevel(Comparable specId)
Get ms level using spectrum id.
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Integer |
getSpectrumPrecursorCharge(Comparable specId)
Get precursor charge of a spectrum.
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double |
getSpectrumPrecursorIntensity(Comparable specId)
Get precursor intensity value using spectrum id.
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double |
getSpectrumPrecursorMz(Comparable specId)
Get precursor m/z value using spectrum id.
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double |
getSumOfIntensity(Comparable specId)
Get sum of intensity value using spectrum id.
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boolean |
isSpectrumBasedOnTitle()
In some cases (WIFF files) the spectrum is referenced using the TITLE instead of using the index.
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void |
populateCache() |
void |
setCachingStrategy(CachingStrategy builder) |
void |
setMode(DataAccessMode mode)
Set the runtime mode
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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, getUid, hasChromatogram, hasDecoyInformation, hasIsotopeLabellingQuantMethods, hasLabelFreeQuantMethods, hasMetaDataInformation, hasPeptide, hasPeptideQuantData, hasPeptideTotalIntensities, hasProtein, hasProteinAmbiguityGroup, hasProteinQuantData, hasProteinSequence, hasProteinTotalIntensities, hasQuantData, hasQuantPeptide, hasSpectrum, indexOfProtein, isIdentifiedSpectrum, proteinsAreInferred, setContentCategories, setInferredProteinGroups, setName, setSource, setType, setUid
public CachedDataAccessController()
public CachedDataAccessController(DataAccessMode mode)
public CachedDataAccessController(Object source, DataAccessMode mode)
public Cache getCache()
public CachingStrategy getCachingStrategy()
public void setCachingStrategy(CachingStrategy builder)
public void populateCache()
public DataAccessMode getMode()
public void setMode(DataAccessMode mode)
mode
- DataAccessModepublic Collection<Comparable> getSpectrumIds()
public Collection<Comparable> getChromatogramIds()
public Collection<Comparable> getProteinIds()
public Spectrum getSpectrumById(Comparable id)
id
- Spectrum idpublic Comparable getSpectrumIdForPeptide(Comparable psmID)
getSpectrumIdForPeptide
in interface MzGraphDataAccess
getSpectrumIdForPeptide
in class AbstractDataAccessController
psmID
- Spectrum-Identification-Item Identifierpublic Chromatogram getChromatogramById(Comparable chromaId)
chromaId
- chromatogram string idpublic Chromatogram getChromatogramById(Comparable id, boolean useCache)
id
- chromatogram iduseCache
- true means to use cachepublic Protein getProteinById(Comparable proteinId)
proteinId
- a string id of Identificationpublic int getNumberOfSpectrumPeaks(Comparable specId)
getNumberOfSpectrumPeaks
in interface MzGraphDataAccess
getNumberOfSpectrumPeaks
in class AbstractDataAccessController
specId
- spectrum id.public int getSpectrumMsLevel(Comparable specId)
getSpectrumMsLevel
in interface MzGraphDataAccess
getSpectrumMsLevel
in class AbstractDataAccessController
specId
- spectrum id.public Integer getSpectrumPrecursorCharge(Comparable specId)
getSpectrumPrecursorCharge
in interface MzGraphDataAccess
getSpectrumPrecursorCharge
in class AbstractDataAccessController
specId
- spectrum id.public Integer getPeptidePrecursorCharge(Comparable proteinId, Comparable peptideId)
getPeptidePrecursorCharge
in interface PeptideDataAccess
getPeptidePrecursorCharge
in class AbstractDataAccessController
proteinId
- identification idpeptideId
- peptid eid, can be the index of the peptide as well.DataAccessException
- data access exceptionpublic double getSpectrumPrecursorMz(Comparable specId)
getSpectrumPrecursorMz
in interface MzGraphDataAccess
getSpectrumPrecursorMz
in class AbstractDataAccessController
specId
- spectrum id.public double getPeptidePrecursorMz(Comparable proteinId, Comparable peptideId)
getPeptidePrecursorMz
in interface PeptideDataAccess
getPeptidePrecursorMz
in class AbstractDataAccessController
proteinId
- identification idpeptideId
- peptid eid, can be the index of the peptide as well.public double getSpectrumPrecursorIntensity(Comparable specId)
getSpectrumPrecursorIntensity
in interface MzGraphDataAccess
getSpectrumPrecursorIntensity
in class AbstractDataAccessController
specId
- spectrum id.public double getSumOfIntensity(Comparable specId)
getSumOfIntensity
in interface MzGraphDataAccess
getSumOfIntensity
in class AbstractDataAccessController
specId
- spectrum id.public String getProteinAccession(Comparable proteinId)
getProteinAccession
in interface ProteinDataAccess
getProteinAccession
in class AbstractDataAccessController
proteinId
- identification id.public String getProteinAccessionVersion(Comparable proteinId)
getProteinAccessionVersion
in interface ProteinDataAccess
getProteinAccessionVersion
in class AbstractDataAccessController
proteinId
- identification id.public double getProteinScore(Comparable proteinId)
getProteinScore
in interface ProteinDataAccess
getProteinScore
in class AbstractDataAccessController
proteinId
- identification id.public double getProteinThreshold(Comparable proteinId)
getProteinThreshold
in interface ProteinDataAccess
getProteinThreshold
in class AbstractDataAccessController
proteinId
- identification id.public SearchDataBase getSearchDatabase(Comparable proteinId)
getSearchDatabase
in interface ProteinDataAccess
getSearchDatabase
in class AbstractDataAccessController
proteinId
- identification id.public String getSearchDatabaseVersion(Comparable proteinId)
getSearchDatabaseVersion
in interface ProteinDataAccess
getSearchDatabaseVersion
in class AbstractDataAccessController
proteinId
- identification id.public Collection<Comparable> getPeptideIds(Comparable proteinId)
getPeptideIds
in interface PeptideDataAccess
getPeptideIds
in class AbstractDataAccessController
proteinId
- identification id.public Peptide getPeptideByIndex(Comparable proteinId, Comparable index)
PeptideDataAccess
getPeptideByIndex
in interface PeptideDataAccess
getPeptideByIndex
in class AbstractDataAccessController
proteinId
- identification idindex
- peptide id, this can be the index of the peptide as well.public Peptide getPeptideByIndex(Comparable proteinId, Comparable index, boolean useCache)
public List<String> getPeptideSequences(Comparable proteinId)
getPeptideSequences
in interface PeptideDataAccess
getPeptideSequences
in class AbstractDataAccessController
proteinId
- identification id.public int getNumberOfPeptides(Comparable proteinId)
getNumberOfPeptides
in interface PeptideDataAccess
getNumberOfPeptides
in class AbstractDataAccessController
proteinId
- identification id.public int getNumberOfUniquePeptides(Comparable proteinId)
getNumberOfUniquePeptides
in interface PeptideDataAccess
getNumberOfUniquePeptides
in class AbstractDataAccessController
proteinId
- identification id.public int getNumberOfPTMs(Comparable proteinId)
getNumberOfPTMs
in interface PeptideDataAccess
getNumberOfPTMs
in class AbstractDataAccessController
proteinId
- identification id.public int getNumberOfPTMs(Comparable proteinId, Comparable peptideId)
getNumberOfPTMs
in interface PeptideDataAccess
getNumberOfPTMs
in class AbstractDataAccessController
proteinId
- identification id.peptideId
- peptide idpublic String getPeptideSequence(Comparable proteinId, Comparable peptideId)
getPeptideSequence
in interface PeptideDataAccess
getPeptideSequence
in class AbstractDataAccessController
proteinId
- identification id.peptideId
- peptide id, this can be the index of the peptide as well.public int getPeptideSequenceStart(Comparable proteinId, Comparable peptideId)
getPeptideSequenceStart
in interface PeptideDataAccess
getPeptideSequenceStart
in class AbstractDataAccessController
proteinId
- identification id.peptideId
- peptide id, this can be the index of the peptide as well.public int getPeptideSequenceEnd(Comparable proteinId, Comparable peptideId)
getPeptideSequenceEnd
in interface PeptideDataAccess
getPeptideSequenceEnd
in class AbstractDataAccessController
proteinId
- identification id.peptideId
- peptide id, this can be the index of the peptide as well.public Comparable getPeptideSpectrumId(Comparable proteinId, Comparable peptideId)
getPeptideSpectrumId
in interface PeptideDataAccess
getPeptideSpectrumId
in class AbstractDataAccessController
proteinId
- identification id.peptideId
- peptide id, this can be the index of the peptide as well.public List<Modification> getPTMs(Comparable proteinId, Comparable peptideId)
getPTMs
in interface PeptideDataAccess
getPTMs
in class AbstractDataAccessController
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptidepublic int getNumberOfFragmentIons(Comparable proteinId, Comparable peptideId)
getNumberOfFragmentIons
in interface PeptideDataAccess
getNumberOfFragmentIons
in class AbstractDataAccessController
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptide as well.public Score getPeptideScore(Comparable proteinId, Comparable peptideId)
getPeptideScore
in interface PeptideDataAccess
getPeptideScore
in class AbstractDataAccessController
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptide as well.public List<uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference> getSearchEngineCvTermReferences()
getSearchEngineCvTermReferences
in interface ProteinDataAccess
getSearchEngineCvTermReferences
in class AbstractDataAccessController
public List<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> getAvailableProteinLevelScores()
getAvailableProteinLevelScores
in interface ProteinDataAccess
getAvailableProteinLevelScores
in class AbstractDataAccessController
public List<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> getAvailablePeptideLevelScores()
getAvailablePeptideLevelScores
in interface PeptideDataAccess
getAvailablePeptideLevelScores
in class AbstractDataAccessController
public uk.ac.ebi.pride.utilities.term.QuantCvTermReference getProteinQuantUnit()
getProteinQuantUnit
in interface QuantDataAccess
getProteinQuantUnit
in class AbstractDataAccessController
public uk.ac.ebi.pride.utilities.term.QuantCvTermReference getPeptideQuantUnit()
getPeptideQuantUnit
in interface QuantDataAccess
getPeptideQuantUnit
in class AbstractDataAccessController
public ExperimentMetaData getExperimentMetaData()
getExperimentMetaData
in interface MetaDataAccess
getExperimentMetaData
in class AbstractDataAccessController
public IdentificationMetaData getIdentificationMetaData()
getIdentificationMetaData
in interface MetaDataAccess
getIdentificationMetaData
in class AbstractDataAccessController
public MzGraphMetaData getMzGraphMetaData()
getMzGraphMetaData
in interface MetaDataAccess
getMzGraphMetaData
in class AbstractDataAccessController
public Collection<Comparable> getProteinAmbiguityGroupIds()
getProteinAmbiguityGroupIds
in interface ProteinGroupDataAccess
getProteinAmbiguityGroupIds
in class AbstractDataAccessController
public ProteinGroup getProteinAmbiguityGroupById(Comparable proteinGroupId)
ProteinGroupDataAccess
getProteinAmbiguityGroupById
in interface ProteinGroupDataAccess
getProteinAmbiguityGroupById
in class AbstractDataAccessController
proteinGroupId
- protein group idpublic List<Peptide> getPeptidesBySpectrum(Comparable specId)
getPeptidesBySpectrum
in interface MzGraphDataAccess
getPeptidesBySpectrum
in class AbstractDataAccessController
specId
- Spectrum Identification Identifierpublic boolean isSpectrumBasedOnTitle()
public List<Comparable> getSpectraDataBasedOnTitle()
public void close()
close
in interface DataAccessController
close
in class AbstractDataAccessController
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.