public abstract class AbstractDataAccessController extends Object implements DataAccessController
DataAccessController.ContentCategory, DataAccessController.Type
CHROMATOGRAM_TYPE, MZGRAPH_TYPE, SPECTRUM_TYPE
Modifier | Constructor and Description |
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protected |
AbstractDataAccessController() |
protected |
AbstractDataAccessController(Object source) |
Modifier and Type | Method and Description |
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void |
close()
shutdown this controller, release all the resources.
|
ParamGroup |
getAdditional() |
List<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> |
getAvailablePeptideLevelScores()
Get a collection of peptide scores in cv term reference format
|
List<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> |
getAvailableProteinLevelScores()
get a list of present protein scores in CV terms
|
Collection<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> |
getAvailableQuantPeptideLevelScores()
Get a collection of peptide scores in cv term reference format
|
Collection<Chromatogram> |
getChromatogramByIndex(int index,
int offset)
Get a collection of chromatograms by its index and offset.
|
int |
getChromatogramIndex(Comparable chromaId)
Get the index of a chromatogram by its id
|
Collection<DataAccessController.ContentCategory> |
getContentCategories()
Return a collection of content categories
|
ExperimentMetaData |
getExperimentMetaData()
Get a meta object
|
Collection<FragmentIon> |
getFragmentIons(Comparable proteinId,
Comparable peptideId)
Get the fragment ions assigned to the peptide.
|
IdentificationMetaData |
getIdentificationMetaData()
Get the MetaData Information for Identification Object.
|
Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> |
getIsotopeLabellingQuantMethods()
Get all the isotope labelling methods
|
Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> |
getLabelFreeQuantMethods()
Get all the label free methods used
|
MzGraphMetaData |
getMzGraphMetaData()
Get MetaData Information for Spectrum Experiment Object
|
String |
getName()
Get the display name for this controller, for GUI
|
int |
getNumberOfChromatograms()
Get number of chromatograms
|
int |
getNumberOfFragmentIons(Comparable proteinId,
Comparable peptideId)
Get the number of fragment ions for a peptide
|
int |
getNumberOfIdentifiedSpectra()
Get the number of identified spectra.
|
int |
getNumberOfPeptides()
Get the total number of peptides
|
int |
getNumberOfPeptides(Comparable proteinId)
Get the number peptides of a identification.
|
int |
getNumberOfPeptidesByRank(int rank)
Get the total number of peptides of a given Rank
|
int |
getNumberOfProteinAmbiguityGroups()
Get the total number of protein ambiguity groups
|
int |
getNumberOfProteins()
Get the total number of protein identifications.
|
int |
getNumberOfPTMs(Comparable proteinId)
Get the number of ptms of a identification.
|
int |
getNumberOfPTMs(Comparable proteinId,
Comparable peptideId)
Get the number of PTMs for a peptide
|
int |
getNumberOfQuantPeptides()
Get the total number of peptides
|
int |
getNumberOfQuantPeptides(Comparable proteinId)
Get the number peptides of a identification.
|
int |
getNumberOfQuantPTMs(Comparable proteinId)
Get the number of ptms of a identification.
|
int |
getNumberOfQuantPTMs(Comparable proteinId,
Comparable peptideId)
Get the number of PTMs for a peptide
|
int |
getNumberOfReagents()
Get the number of reagents
|
int |
getNumberOfSpectra()
Get the number of spectra.
|
int |
getNumberOfSpectrumPeaks(Comparable specId)
Get the number peaks of a spectrum
|
int |
getNumberOfSubstitutionPTMs(Comparable proteinId)
Get the number of Substitution ptms of a identification.
|
int |
getNumberOfSubstitutionPTMs(Comparable proteinId,
Comparable peptideId)
Get the number of Substitution PTMs for a peptide
|
int |
getNumberOfUniquePeptides(Comparable proteinId)
Get the number of unique peptides of a identification.
|
int |
getNumberOfUniqueQuantPeptides(Comparable proteinId)
Get the number of unique peptides of a identification.
|
Peptide |
getPeptideByIndex(Comparable proteinId,
Comparable index)
This is convenient method for accessing peptide.
|
Collection<PeptideEvidence> |
getPeptideEvidences(Comparable proteinId,
Comparable peptideId)
Get all Peptide Evidence for a Peptide Identification
|
Collection<Comparable> |
getPeptideIds(Comparable proteinId)
Get a collection of peptide ids belong to the identification.
|
Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> |
getPeptideIsotopeLabellingQuantMethods()
Get the isotope labelling methods at the peptide level
|
Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> |
getPeptideLabelFreeQuantMethods()
Get the label free methods at the peptide identification level
|
Integer |
getPeptidePrecursorCharge(Comparable identId,
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
|
double |
getPeptidePrecursorMz(Comparable proteinId,
Comparable peptideId)
Get precursor m/z on peptide level
Note: sometimes, precursor m/z 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
|
Quantification |
getPeptideQuantData(Comparable proteinId,
Comparable peptideId)
Get quantitative data related to a given peptide
|
QuantScore |
getPeptideQuantStudyData(Comparable proteinId,
Comparable peptideId)
Retrieve the Quantitation Score of peptides in Study Variables
|
uk.ac.ebi.pride.utilities.term.QuantCvTermReference |
getPeptideQuantUnit()
Get the unit for peptide identification
|
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
|
Score |
getPeptideScore(Comparable proteinId,
Comparable peptideId)
Get peptide score generated by search engine.
|
String |
getPeptideSequence(Comparable proteinId,
Comparable peptideId)
Get peptide sequence according to identification id and peptide id.
|
int |
getPeptideSequenceEnd(Comparable proteinId,
Comparable peptideId)
Get peptide sequence stop
|
List<String> |
getPeptideSequences(Comparable proteinId)
This method is to get a list of redundant peptide sequences
|
int |
getPeptideSequenceStart(Comparable proteinId,
Comparable peptideId)
Get peptide sequence start
|
Comparable |
getPeptideSpectrumId(Comparable proteinId,
Comparable peptideId)
Get peptide's spectrum id
|
double |
getPeptideTheoreticalMz(Comparable proteinId,
Comparable peptideId)
Get The Peptide Theoretical Mz from the file
Note: sometimes, precursor m/z 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
|
String |
getProteinAccession(Comparable proteinId)
Get the protein accession of a identification
|
String |
getProteinAccessionVersion(Comparable proteinId)
Get the protein accession version of a identification
|
ProteinGroup |
getProteinAmbiguityGroupById(Comparable proteinGroupId)
Get protein ambiguity group using protein group id
|
Collection<Comparable> |
getProteinAmbiguityGroupIds()
Get a collection of identification group ids
|
Collection<Protein> |
getProteinByIndex(int index,
int offset) |
double |
getProteinCoverage(Comparable proteinId)
The Coverage is compute as the number of identified (AminoAcid/TotalAminoAcids)*100
|
Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> |
getProteinIsotopeLabellingQuantMethods()
Get the isotope labelling methods at the protein level
|
Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> |
getProteinLabelFreeQuantMethods()
Get the label free methods at the protein identification level
|
Quantification |
getProteinQuantData(Comparable proteinId)
Get quantitative data related to a given protein
|
QuantScore |
getProteinQuantStudyData(Comparable proteinId)
Return the Quantitation Score for Study variables approach.
|
uk.ac.ebi.pride.utilities.term.QuantCvTermReference |
getProteinQuantUnit()
Get the unit for protein identifications
|
double |
getProteinScore(Comparable proteinId)
Get the score of a identification.
|
Score |
getProteinScores(Comparable proteinId)
Get protein identification score
|
DBSequence |
getProteinSequence(Comparable proteinId)
Get the sequence of the Identified Protein
|
double |
getProteinThreshold(Comparable proteinId)
Get the threshold of a identification.
|
List<Modification> |
getPTMs(Comparable proteinId,
Comparable peptideId)
Get the ptms assigned to a peptide
|
Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> |
getQuantMethods()
Get quantitative method type
|
QuantPeptide |
getQuantPeptideByIndex(Comparable proteinId,
Comparable peptideId)
This is convenient method for accessing peptide.
|
Collection<PeptideEvidence> |
getQuantPeptideEvidences(Comparable proteinId,
Comparable peptideId)
Get all Peptide Evidence for a Peptide Identification
|
Collection<Comparable> |
getQuantPeptideIds(Comparable proteinId)
Get a collection of peptide ids belong to the identification.
|
QuantScore |
getQuantPeptideQuantScore(Comparable proteinId,
Comparable peptideId)
Get peptide score generated by search engine.
|
Score |
getQuantPeptideScore(Comparable proteinId,
Comparable peptideId)
Get peptide score generated by search engine.
|
String |
getQuantPeptideSequence(Comparable proteinId,
Comparable peptideId)
Get peptide sequence according to identification id and peptide id.
|
Collection<String> |
getQuantPeptideSequences(Comparable proteinId)
This method is to get a list of redundant peptide sequences
|
Comparable |
getQuantPeptideSpectrumId(Comparable proteinId,
Comparable peptideId)
Get peptide's spectrum id
|
Collection<Modification> |
getQuantPTMs(Comparable proteinId,
Comparable peptideId)
Get the ptms assigned to a peptide
|
QuantitativeSample |
getQuantSample()
Get the mapping between sub samples and reagents
|
int |
getReferenceSubSampleIndex()
Get reference reagent's sub sample index
|
Collection<Sample> |
getSamples() |
SearchDataBase |
getSearchDatabase(Comparable proteinId)
Get the search database of a identification
|
String |
getSearchDatabaseVersion(Comparable proteinId)
Get the search database version of a identification
|
List<uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference> |
getSearchEngineCvTermReferences()
Get the search engine of a identification
|
Object |
getSource()
Get the original data source object
|
Collection<Spectrum> |
getSpectraByIndex(int index,
int offset)
Get a collection of spectra by its index and offset.
|
Comparable |
getSpectrumIdForPeptide(Comparable psmID)
Convert the PSM id to spectrum ID
|
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 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.
|
Map<Comparable,StudyVariable> |
getStudyVariables()
In mzTab files the information of Quantitation is store in StudyVariables and not in Samples
|
Collection<SubstitutionModification> |
getSubstitutionPTMs(Comparable proteinId,
Comparable peptideId)
Get the ptms assigned to a peptide
|
double |
getSumOfIntensity(Comparable specId)
Get the sum of intensity of a spectrum.
|
DataAccessController.Type |
getType()
Get the type of database access controller.
|
String |
getUid()
Get the unique id represent the uniqueness of the data source
|
boolean |
hasChromatogram()
Whether this controller contains chromatogram.
|
boolean |
hasDecoyInformation()
This function return true if the controller contains decoy information and false if the controller do not contain decoy information.
|
boolean |
hasIsotopeLabellingQuantMethods()
Check whether the experiment contains quantitative data using isotope labelling methods
|
boolean |
hasLabelFreeQuantMethods()
Check whether the experiment contains quantitative data using label free methods
|
boolean |
hasMetaDataInformation()
This function give the user the possibility to know if the controller contains
MetaData.
|
boolean |
hasPeptide()
Whether this controller contains peptides
|
boolean |
hasPeptideQuantData()
Check whether the experiment contains quantitative data at the peptide level
|
boolean |
hasPeptideTotalIntensities()
Check whether the experiment contains total intensities at the protein level
|
boolean |
hasProtein()
Whether this controller contains identifications
|
boolean |
hasProteinAmbiguityGroup()
Whether this controller contains protein groups information
|
boolean |
hasProteinQuantData()
Check whether the experiment contains quantitative data at the protein level
|
boolean |
hasProteinSequence()
Whether this controller contains protein sequences
|
boolean |
hasProteinTotalIntensities()
Check whether the experiment contains total intensities at the protein level
|
boolean |
hasQuantData()
Check whether the experiment contains quantitative data
|
boolean |
hasQuantPeptide()
Whether this controller contains peptides
|
boolean |
hasSpectrum()
Whether this controller contains spectra
|
int |
indexOfProtein(Comparable proteinId)
Get the index of identification by its id
|
boolean |
isIdentifiedSpectrum(Comparable specId)
Check whether the given spectrum is identified.
|
boolean |
proteinsAreInferred()
returns true if the proteins are inferred externally
|
void |
setContentCategories(DataAccessController.ContentCategory... categories) |
void |
setInferredProteinGroups(Map<Comparable,Map<Comparable,List<Comparable>>> proteinGroups)
This method sets the protein groups calculated by a protein inference.
|
void |
setName(String name) |
void |
setSource(Object src) |
void |
setType(DataAccessController.Type type) |
void |
setUid(String uid) |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getChromatogramById, getChromatogramIds, getSpectrumById, getSpectrumIds
getProteinById, getProteinIds
protected AbstractDataAccessController()
protected AbstractDataAccessController(Object source)
public String getUid()
DataAccessController
getUid
in interface DataAccessController
public void setUid(String uid)
public String getName()
DataAccessController
getName
in interface DataAccessController
public void setName(String name)
public DataAccessController.Type getType()
DataAccessController
getType
in interface DataAccessController
public void setType(DataAccessController.Type type)
public Collection<DataAccessController.ContentCategory> getContentCategories()
DataAccessController
getContentCategories
in interface DataAccessController
public void setContentCategories(DataAccessController.ContentCategory... categories)
public Object getSource()
DataAccessController
getSource
in interface DataAccessController
public void setSource(Object src)
public void close()
DataAccessController
close
in interface DataAccessController
public ExperimentMetaData getExperimentMetaData()
MetaDataAccess
getExperimentMetaData
in interface MetaDataAccess
public IdentificationMetaData getIdentificationMetaData()
MetaDataAccess
getIdentificationMetaData
in interface MetaDataAccess
public MzGraphMetaData getMzGraphMetaData()
MetaDataAccess
getMzGraphMetaData
in interface MetaDataAccess
public Collection<Sample> getSamples()
public ParamGroup getAdditional()
public boolean hasSpectrum()
MzGraphDataAccess
hasSpectrum
in interface MzGraphDataAccess
public boolean hasProteinSequence()
ProteinDataAccess
hasProteinSequence
in interface ProteinDataAccess
public boolean hasDecoyInformation()
ProteinDataAccess
hasDecoyInformation
in interface ProteinDataAccess
public int getNumberOfSpectra()
MzGraphDataAccess
getNumberOfSpectra
in interface MzGraphDataAccess
public int getNumberOfIdentifiedSpectra()
MzGraphDataAccess
getNumberOfIdentifiedSpectra
in interface MzGraphDataAccess
public int getSpectrumIndex(Comparable id)
MzGraphDataAccess
getSpectrumIndex
in interface MzGraphDataAccess
id
- spectrum idpublic Collection<Spectrum> getSpectraByIndex(int index, int offset)
MzGraphDataAccess
getSpectraByIndex
in interface MzGraphDataAccess
index
- the start index of the spectrum.offset
- the max number of spectra to get.public boolean isIdentifiedSpectrum(Comparable specId)
MzGraphDataAccess
isIdentifiedSpectrum
in interface MzGraphDataAccess
specId
- spectrum idpublic List<Peptide> getPeptidesBySpectrum(Comparable specId)
getPeptidesBySpectrum
in interface MzGraphDataAccess
specId
- Spectrum Identifierpublic Comparable getSpectrumIdForPeptide(Comparable psmID)
MzGraphDataAccess
getSpectrumIdForPeptide
in interface MzGraphDataAccess
psmID
- Spectrum-Identification-Item Identifierpublic int getNumberOfSpectrumPeaks(Comparable specId)
MzGraphDataAccess
getNumberOfSpectrumPeaks
in interface MzGraphDataAccess
specId
- spectrum id.public int getSpectrumMsLevel(Comparable specId)
MzGraphDataAccess
getSpectrumMsLevel
in interface MzGraphDataAccess
specId
- spectrum id.public Integer getSpectrumPrecursorCharge(Comparable specId)
getSpectrumPrecursorCharge
in interface MzGraphDataAccess
specId
- spectrum id.public double getSpectrumPrecursorMz(Comparable specId)
MzGraphDataAccess
getSpectrumPrecursorMz
in interface MzGraphDataAccess
specId
- spectrum id.public Integer getPeptidePrecursorCharge(Comparable identId, Comparable peptideId)
getPeptidePrecursorCharge
in interface PeptideDataAccess
identId
- identification idpeptideId
- peptid eid, can be the index of the peptide as well.DataAccessException
- data access exceptionpublic double getPeptidePrecursorMz(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getPeptidePrecursorMz
in interface PeptideDataAccess
proteinId
- identification idpeptideId
- peptid eid, can be the index of the peptide as well.public double getPeptideTheoreticalMz(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getPeptideTheoreticalMz
in interface PeptideDataAccess
proteinId
- identification idpeptideId
- peptid eid, can be the index of the peptide as well.public double getSpectrumPrecursorIntensity(Comparable specId)
MzGraphDataAccess
getSpectrumPrecursorIntensity
in interface MzGraphDataAccess
specId
- spectrum id.public double getSumOfIntensity(Comparable specId)
MzGraphDataAccess
getSumOfIntensity
in interface MzGraphDataAccess
specId
- spectrum id.public boolean hasChromatogram()
MzGraphDataAccess
hasChromatogram
in interface MzGraphDataAccess
public int getNumberOfChromatograms()
MzGraphDataAccess
getNumberOfChromatograms
in interface MzGraphDataAccess
public int getChromatogramIndex(Comparable chromaId)
MzGraphDataAccess
getChromatogramIndex
in interface MzGraphDataAccess
chromaId
- chromatogram idpublic Collection<Chromatogram> getChromatogramByIndex(int index, int offset)
MzGraphDataAccess
getChromatogramByIndex
in interface MzGraphDataAccess
index
- index of the starting chromatogram.offset
- the number of chromatogram to get.public boolean hasProtein()
ProteinDataAccess
hasProtein
in interface ProteinDataAccess
public final boolean proteinsAreInferred()
public final void setInferredProteinGroups(Map<Comparable,Map<Comparable,List<Comparable>>> proteinGroups)
ProteinGroupDataAccess
After the protein groups are set to "!= null", these protein groups are returned and all other implementation of protein groups are ignored.
the groups are rebuild by using the mapping PAG_ID -> (Protein_ID -> [Peptide_IDs])
if the peptide_IDs-list is null, then all peptides are used of the protein (no filtering or all passed filtering)
setInferredProteinGroups
in interface ProteinGroupDataAccess
proteinGroups
- A java.lang.Map of protein groups to be setpublic boolean hasProteinAmbiguityGroup()
ProteinGroupDataAccess
hasProteinAmbiguityGroup
in interface ProteinGroupDataAccess
public boolean hasPeptide()
PeptideDataAccess
hasPeptide
in interface PeptideDataAccess
public int getNumberOfProteins()
ProteinDataAccess
getNumberOfProteins
in interface ProteinDataAccess
public int getNumberOfProteinAmbiguityGroups()
ProteinGroupDataAccess
getNumberOfProteinAmbiguityGroups
in interface ProteinGroupDataAccess
public Collection<Comparable> getProteinAmbiguityGroupIds()
ProteinGroupDataAccess
getProteinAmbiguityGroupIds
in interface ProteinGroupDataAccess
public ProteinGroup getProteinAmbiguityGroupById(Comparable proteinGroupId)
ProteinGroupDataAccess
getProteinAmbiguityGroupById
in interface ProteinGroupDataAccess
proteinGroupId
- protein group idpublic int indexOfProtein(Comparable proteinId)
ProteinDataAccess
indexOfProtein
in interface ProteinDataAccess
proteinId
- identification idpublic Collection<Protein> getProteinByIndex(int index, int offset)
public String getProteinAccession(Comparable proteinId)
ProteinDataAccess
getProteinAccession
in interface ProteinDataAccess
proteinId
- identification id.public String getProteinAccessionVersion(Comparable proteinId)
ProteinDataAccess
getProteinAccessionVersion
in interface ProteinDataAccess
proteinId
- identification id.public double getProteinScore(Comparable proteinId)
ProteinDataAccess
getProteinScore
in interface ProteinDataAccess
proteinId
- identification id.public DBSequence getProteinSequence(Comparable proteinId)
ProteinDataAccess
getProteinSequence
in interface ProteinDataAccess
proteinId
- identification Idpublic double getProteinThreshold(Comparable proteinId)
ProteinDataAccess
getProteinThreshold
in interface ProteinDataAccess
proteinId
- identification id.public SearchDataBase getSearchDatabase(Comparable proteinId)
ProteinDataAccess
getSearchDatabase
in interface ProteinDataAccess
proteinId
- identification id.public String getSearchDatabaseVersion(Comparable proteinId)
ProteinDataAccess
getSearchDatabaseVersion
in interface ProteinDataAccess
proteinId
- identification idpublic List<uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference> getSearchEngineCvTermReferences()
ProteinDataAccess
getSearchEngineCvTermReferences
in interface ProteinDataAccess
public List<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> getAvailableProteinLevelScores()
ProteinDataAccess
getAvailableProteinLevelScores
in interface ProteinDataAccess
public List<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> getAvailablePeptideLevelScores()
PeptideDataAccess
getAvailablePeptideLevelScores
in interface PeptideDataAccess
public Score getProteinScores(Comparable proteinId)
ProteinDataAccess
getProteinScores
in interface ProteinDataAccess
proteinId
- Protein Idpublic double getProteinCoverage(Comparable proteinId)
getProteinCoverage
in interface ProteinDataAccess
proteinId
- The protein identification Idpublic Collection<Comparable> getPeptideIds(Comparable proteinId)
PeptideDataAccess
getPeptideIds
in interface PeptideDataAccess
proteinId
- identification idpublic Peptide getPeptideByIndex(Comparable proteinId, Comparable index)
PeptideDataAccess
getPeptideByIndex
in interface PeptideDataAccess
proteinId
- identification idindex
- peptide id, this can be the index of the peptide as well.public List<String> getPeptideSequences(Comparable proteinId)
PeptideDataAccess
getPeptideSequences
in interface PeptideDataAccess
proteinId
- identification idpublic Collection<PeptideEvidence> getPeptideEvidences(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getPeptideEvidences
in interface PeptideDataAccess
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptide as well.public int getNumberOfPeptides(Comparable proteinId)
PeptideDataAccess
getNumberOfPeptides
in interface PeptideDataAccess
proteinId
- identification id.public int getNumberOfPeptides()
PeptideDataAccess
getNumberOfPeptides
in interface PeptideDataAccess
public int getNumberOfPeptidesByRank(int rank)
PeptideDataAccess
getNumberOfPeptidesByRank
in interface PeptideDataAccess
public int getNumberOfUniquePeptides(Comparable proteinId)
PeptideDataAccess
getNumberOfUniquePeptides
in interface PeptideDataAccess
proteinId
- identification id.public int getNumberOfPTMs(Comparable proteinId)
PeptideDataAccess
getNumberOfPTMs
in interface PeptideDataAccess
proteinId
- identification id.public int getNumberOfPTMs(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getNumberOfPTMs
in interface PeptideDataAccess
proteinId
- identification idpeptideId
- peptide idpublic String getPeptideSequence(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getPeptideSequence
in interface PeptideDataAccess
proteinId
- identification idpeptideId
- peptide id, this can be the index of the peptide as well.public int getPeptideRank(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getPeptideRank
in interface PeptideDataAccess
proteinId
- protein idpeptideId
- peptide idpublic int getPeptideSequenceStart(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getPeptideSequenceStart
in interface PeptideDataAccess
proteinId
- identification idpeptideId
- peptide id, this can be the index of the peptide as well.public int getPeptideSequenceEnd(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getPeptideSequenceEnd
in interface PeptideDataAccess
proteinId
- identification idpeptideId
- peptide id, this can be the index of the peptide as well.public Comparable getPeptideSpectrumId(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getPeptideSpectrumId
in interface PeptideDataAccess
proteinId
- identification idpeptideId
- peptide id, this can be the index of the peptide as well.public List<Modification> getPTMs(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getPTMs
in interface PeptideDataAccess
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptidepublic Collection<SubstitutionModification> getSubstitutionPTMs(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getSubstitutionPTMs
in interface PeptideDataAccess
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptidepublic int getNumberOfSubstitutionPTMs(Comparable proteinId)
PeptideDataAccess
getNumberOfSubstitutionPTMs
in interface PeptideDataAccess
proteinId
- identification id.public int getNumberOfSubstitutionPTMs(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getNumberOfSubstitutionPTMs
in interface PeptideDataAccess
proteinId
- identification idpeptideId
- peptide idpublic int getNumberOfFragmentIons(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getNumberOfFragmentIons
in interface PeptideDataAccess
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptide as well.public Collection<FragmentIon> getFragmentIons(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getFragmentIons
in interface PeptideDataAccess
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptide as well.public Score getPeptideScore(Comparable proteinId, Comparable peptideId)
PeptideDataAccess
getPeptideScore
in interface PeptideDataAccess
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptide as well.public boolean hasQuantData()
QuantDataAccess
hasQuantData
in interface QuantDataAccess
public boolean hasProteinQuantData()
QuantDataAccess
hasProteinQuantData
in interface QuantDataAccess
public boolean hasPeptideQuantData()
QuantDataAccess
hasPeptideQuantData
in interface QuantDataAccess
public boolean hasProteinTotalIntensities()
QuantDataAccess
hasProteinTotalIntensities
in interface QuantDataAccess
public boolean hasPeptideTotalIntensities()
QuantDataAccess
hasPeptideTotalIntensities
in interface QuantDataAccess
public boolean hasLabelFreeQuantMethods()
QuantDataAccess
hasLabelFreeQuantMethods
in interface QuantDataAccess
public boolean hasIsotopeLabellingQuantMethods()
QuantDataAccess
hasIsotopeLabellingQuantMethods
in interface QuantDataAccess
public Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> getQuantMethods()
QuantDataAccess
getQuantMethods
in interface QuantDataAccess
public Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> getLabelFreeQuantMethods()
QuantDataAccess
getLabelFreeQuantMethods
in interface QuantDataAccess
public Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> getProteinLabelFreeQuantMethods()
QuantDataAccess
getProteinLabelFreeQuantMethods
in interface QuantDataAccess
public Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> getPeptideLabelFreeQuantMethods()
QuantDataAccess
getPeptideLabelFreeQuantMethods
in interface QuantDataAccess
public Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> getIsotopeLabellingQuantMethods()
QuantDataAccess
getIsotopeLabellingQuantMethods
in interface QuantDataAccess
public Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> getProteinIsotopeLabellingQuantMethods()
QuantDataAccess
getProteinIsotopeLabellingQuantMethods
in interface QuantDataAccess
public Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> getPeptideIsotopeLabellingQuantMethods()
QuantDataAccess
getPeptideIsotopeLabellingQuantMethods
in interface QuantDataAccess
public int getNumberOfReagents()
QuantDataAccess
getNumberOfReagents
in interface QuantDataAccess
public int getReferenceSubSampleIndex()
QuantDataAccess
getReferenceSubSampleIndex
in interface QuantDataAccess
public QuantitativeSample getQuantSample()
QuantDataAccess
getQuantSample
in interface QuantDataAccess
public uk.ac.ebi.pride.utilities.term.QuantCvTermReference getProteinQuantUnit()
QuantDataAccess
getProteinQuantUnit
in interface QuantDataAccess
public uk.ac.ebi.pride.utilities.term.QuantCvTermReference getPeptideQuantUnit()
QuantDataAccess
getPeptideQuantUnit
in interface QuantDataAccess
public Quantification getProteinQuantData(Comparable proteinId)
QuantDataAccess
getProteinQuantData
in interface QuantDataAccess
proteinId
- protein identification idpublic Quantification getPeptideQuantData(Comparable proteinId, Comparable peptideId)
QuantDataAccess
getPeptideQuantData
in interface QuantDataAccess
proteinId
- protein identification idpeptideId
- peptide idpublic boolean hasMetaDataInformation()
MetaDataAccess
hasMetaDataInformation
in interface MetaDataAccess
public Map<Comparable,StudyVariable> getStudyVariables()
QuantDataAccess
getStudyVariables
in interface QuantDataAccess
public QuantScore getProteinQuantStudyData(Comparable proteinId)
QuantDataAccess
getProteinQuantStudyData
in interface QuantDataAccess
proteinId
- Protein IDpublic QuantScore getPeptideQuantStudyData(Comparable proteinId, Comparable peptideId)
QuantDataAccess
getPeptideQuantStudyData
in interface QuantDataAccess
proteinId
- Protein IdentifierpeptideId
- Peptide Identifierpublic Collection<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> getAvailableQuantPeptideLevelScores()
QuantDataAccess
getAvailableQuantPeptideLevelScores
in interface QuantDataAccess
public boolean hasQuantPeptide()
QuantDataAccess
hasQuantPeptide
in interface QuantDataAccess
public Collection<Comparable> getQuantPeptideIds(Comparable proteinId)
QuantDataAccess
getQuantPeptideIds
in interface QuantDataAccess
proteinId
- identification idpublic QuantPeptide getQuantPeptideByIndex(Comparable proteinId, Comparable peptideId)
QuantDataAccess
getQuantPeptideByIndex
in interface QuantDataAccess
proteinId
- identification idpeptideId
- peptide id, this can be the index of the peptide as well.public Collection<String> getQuantPeptideSequences(Comparable proteinId)
QuantDataAccess
getQuantPeptideSequences
in interface QuantDataAccess
proteinId
- identification idpublic String getQuantPeptideSequence(Comparable proteinId, Comparable peptideId)
QuantDataAccess
getQuantPeptideSequence
in interface QuantDataAccess
proteinId
- identification idpeptideId
- peptide id, this can be the index of the peptide as well.public Comparable getQuantPeptideSpectrumId(Comparable proteinId, Comparable peptideId)
QuantDataAccess
getQuantPeptideSpectrumId
in interface QuantDataAccess
proteinId
- identification idpeptideId
- peptide id, this can be the index of the peptide as well.public int getNumberOfQuantPeptides()
QuantDataAccess
getNumberOfQuantPeptides
in interface QuantDataAccess
public int getNumberOfQuantPeptides(Comparable proteinId)
QuantDataAccess
getNumberOfQuantPeptides
in interface QuantDataAccess
proteinId
- identification id.public int getNumberOfUniqueQuantPeptides(Comparable proteinId)
QuantDataAccess
getNumberOfUniqueQuantPeptides
in interface QuantDataAccess
proteinId
- identification id.public int getNumberOfQuantPTMs(Comparable proteinId)
QuantDataAccess
getNumberOfQuantPTMs
in interface QuantDataAccess
proteinId
- identification id.public int getNumberOfQuantPTMs(Comparable proteinId, Comparable peptideId)
QuantDataAccess
getNumberOfQuantPTMs
in interface QuantDataAccess
proteinId
- identification idpeptideId
- peptide idpublic Collection<Modification> getQuantPTMs(Comparable proteinId, Comparable peptideId)
QuantDataAccess
getQuantPTMs
in interface QuantDataAccess
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptidepublic Score getQuantPeptideScore(Comparable proteinId, Comparable peptideId)
QuantDataAccess
getQuantPeptideScore
in interface QuantDataAccess
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptide as well.public QuantScore getQuantPeptideQuantScore(Comparable proteinId, Comparable peptideId)
QuantDataAccess
getQuantPeptideQuantScore
in interface QuantDataAccess
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptide as well.public Collection<PeptideEvidence> getQuantPeptideEvidences(Comparable proteinId, Comparable peptideId)
QuantDataAccess
getQuantPeptideEvidences
in interface QuantDataAccess
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptide as well.Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.