public abstract class ReferencedIdentificationController extends CachedDataAccessController
DataAccessController.ContentCategory, DataAccessController.Type
Modifier and Type | Field and Description |
---|---|
protected Map<Comparable,DataAccessController> |
msDataAccessControllers |
CHROMATOGRAM_TYPE, MZGRAPH_TYPE, SPECTRUM_TYPE
Constructor and Description |
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ReferencedIdentificationController(File file,
DataAccessMode cacheAndSource) |
Modifier and Type | Method and Description |
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void |
addMSController(List<File> dataAccessControllerFiles)
Add a List of MS Files to the mzidentml.
|
void |
addMSController(Map<SpectraData,File> spectraDataFileMap)
Check if the File format is supported and the spectrum Id and add a Set of DataAccessControllers.
|
boolean |
addNewMSController(Map<SpectraData,File> spectraDataFileMap,
Map<Comparable,File> newFiles,
Map<Comparable,String> fileTypes) |
protected void |
cacheProtein(Protein ident) |
Map<SpectraData,File> |
checkMScontrollers(List<File> msIdentMLFiles)
Check if the ms File is supported and match with some of the par of the name in the Spectra Files
This method should be used in high-throughput, when you add different files.
|
void |
clearMSControllers() |
int |
getNumberOfIdentifiedSpectra()
Get the number of Spectra Identified in the DataAccessController
|
int |
getNumberOfSpectra()
Return the number of Spectra in the DataAccessController
|
Integer |
getNumberOfSpectrabySpectraData(SpectraData spectraData)
Get the number of Spectra by File associated with the mzidentml
|
Peptide |
getPeptideByIndex(Comparable proteinId,
Comparable index,
boolean useCache)
Get peptide using a given identification id and a given peptide index
|
int |
getPeptideRank(Comparable proteinId,
Comparable peptideId)
Convenient method for accessing the rank of the peptide
|
List<Peptide> |
getPeptidesBySpectrum(Comparable specId)
Retrieve the Identified Peptides related with one spectrum
|
Comparable |
getPeptideSpectrumId(Comparable proteinId,
Comparable peptideId)
Get peptide spectrum id using identification id and peptide id.
|
Map<SpectraData,DataAccessController> |
getSpectraDataMSControllers() |
Map<SpectraData,File> |
getSpectraDataMSFiles()
Get the Spectra Data Map with the corresponding File.
|
Spectrum |
getSpectrumById(Comparable id,
boolean useCache)
Get spectrum using a spectrumIdentification id, gives the option to choose whether to
use cache.
|
List<DataAccessController> |
getSpectrumDataAccessControllers() |
Comparable |
getSpectrumIdBySpectrumIdentificationItemId(Comparable id) |
Collection<Comparable> |
getSpectrumIds()
Get spectrum ids from cache
|
List<Comparable> |
getSupportedSpectraData() |
boolean |
hasProteinAmbiguityGroup()
Check if the PROTEIN_GROUP Cache contains any element
|
boolean |
hasSpectrum()
If the spectrum information associated with the identification files is provided
then the mzidentml contains spectra.
|
boolean |
isIdentifiedSpectrum(Comparable specId)
Is identified Spectrum return true if the spectrum was identified
|
protected boolean |
isSpectraDataSupported(SpectraData spectraData) |
close, getAvailablePeptideLevelScores, getAvailableProteinLevelScores, getCache, getCachingStrategy, getChromatogramById, getChromatogramById, getChromatogramIds, getExperimentMetaData, getIdentificationMetaData, getMode, getMzGraphMetaData, getNumberOfFragmentIons, getNumberOfPeptides, getNumberOfPTMs, getNumberOfPTMs, getNumberOfSpectrumPeaks, getNumberOfUniquePeptides, getPeptideByIndex, getPeptideIds, getPeptidePrecursorCharge, getPeptidePrecursorMz, getPeptideQuantUnit, getPeptideScore, getPeptideSequence, getPeptideSequenceEnd, getPeptideSequences, getPeptideSequenceStart, 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, getNumberOfPeptides, getNumberOfPeptidesByRank, getNumberOfProteinAmbiguityGroups, getNumberOfProteins, getNumberOfQuantPeptides, getNumberOfQuantPeptides, getNumberOfQuantPTMs, getNumberOfQuantPTMs, getNumberOfReagents, getNumberOfSubstitutionPTMs, getNumberOfSubstitutionPTMs, getNumberOfUniqueQuantPeptides, getPeptideEvidences, getPeptideIsotopeLabellingQuantMethods, getPeptideLabelFreeQuantMethods, getPeptideQuantData, getPeptideQuantStudyData, 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, hasProteinQuantData, hasProteinSequence, hasProteinTotalIntensities, hasQuantData, hasQuantPeptide, indexOfProtein, proteinsAreInferred, setContentCategories, setInferredProteinGroups, setName, setSource, setType, setUid
protected Map<Comparable,DataAccessController> msDataAccessControllers
public ReferencedIdentificationController(File file, DataAccessMode cacheAndSource)
public int getNumberOfSpectra()
getNumberOfSpectra
in interface MzGraphDataAccess
getNumberOfSpectra
in class AbstractDataAccessController
protected void cacheProtein(Protein ident)
public List<DataAccessController> getSpectrumDataAccessControllers()
public Integer getNumberOfSpectrabySpectraData(SpectraData spectraData)
spectraData
- The SpectraData file with the Spectrapublic Map<SpectraData,DataAccessController> getSpectraDataMSControllers()
public Map<SpectraData,File> getSpectraDataMSFiles()
public List<Comparable> getSupportedSpectraData()
protected boolean isSpectraDataSupported(SpectraData spectraData)
public void addMSController(List<File> dataAccessControllerFiles)
dataAccessControllerFiles
- A List of DataAccessControllers related with the MzIdentMLpublic Map<SpectraData,File> checkMScontrollers(List<File> msIdentMLFiles)
msIdentMLFiles
- List of the MS files related with the MZIdentMLpublic void addMSController(Map<SpectraData,File> spectraDataFileMap)
spectraDataFileMap
- A Map of SpectraData Files.public void clearMSControllers()
public boolean addNewMSController(Map<SpectraData,File> spectraDataFileMap, Map<Comparable,File> newFiles, Map<Comparable,String> fileTypes)
public boolean isIdentifiedSpectrum(Comparable specId)
isIdentifiedSpectrum
in interface MzGraphDataAccess
isIdentifiedSpectrum
in class AbstractDataAccessController
specId
- The Spectrum Identification Item, it Can be an spectrum Identification Item or a Peptide IDpublic List<Peptide> getPeptidesBySpectrum(Comparable specId)
getPeptidesBySpectrum
in interface MzGraphDataAccess
getPeptidesBySpectrum
in class CachedDataAccessController
specId
- The spectrum-identification identifierpublic Collection<Comparable> getSpectrumIds()
CachedDataAccessController
getSpectrumIds
in interface MzGraphDataAccess
getSpectrumIds
in class CachedDataAccessController
public Spectrum getSpectrumById(Comparable id, boolean useCache)
id
- spectrum Identification IDuseCache
- true means to use cachepublic boolean hasSpectrum()
hasSpectrum
in interface MzGraphDataAccess
hasSpectrum
in class AbstractDataAccessController
public int getNumberOfIdentifiedSpectra()
getNumberOfIdentifiedSpectra
in interface MzGraphDataAccess
getNumberOfIdentifiedSpectra
in class AbstractDataAccessController
public Comparable getSpectrumIdBySpectrumIdentificationItemId(Comparable id)
public Comparable getPeptideSpectrumId(Comparable proteinId, Comparable peptideId)
CachedDataAccessController
getPeptideSpectrumId
in interface PeptideDataAccess
getPeptideSpectrumId
in class CachedDataAccessController
proteinId
- identification id.peptideId
- peptide id, this can be the index of the peptide as well.public Peptide getPeptideByIndex(Comparable proteinId, Comparable index, boolean useCache)
getPeptideByIndex
in class CachedDataAccessController
index
- peptide indexuseCache
- whether to use cachepublic int getPeptideRank(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getPeptideRank
in interface PeptideDataAccess
getPeptideRank
in class AbstractDataAccessController
proteinId
- protein idpeptideId
- peptide idpublic boolean hasProteinAmbiguityGroup()
hasProteinAmbiguityGroup
in interface ProteinGroupDataAccess
hasProteinAmbiguityGroup
in class AbstractDataAccessController
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.