public interface PeptideDataAccess
Modifier and Type | Method and Description |
---|---|
Collection<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> |
getAvailablePeptideLevelScores()
Get a collection of peptide scores in cv term reference format
|
Collection<FragmentIon> |
getFragmentIons(Comparable proteinId,
Comparable peptideId)
Get the fragment ions assigned to the peptide.
|
int |
getNumberOfFragmentIons(Comparable proteinId,
Comparable peptideId)
Get the number of fragment ions for a peptide
|
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 |
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 |
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.
|
Peptide |
getPeptideByIndex(Comparable proteinId,
Comparable peptideId)
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.
|
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
|
int |
getPeptideRank(Comparable proteinId,
Comparable peptideId)
Convenient method for accessing the rank of the peptide
|
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
|
Collection<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
|
Collection<Modification> |
getPTMs(Comparable proteinId,
Comparable peptideId)
Get the ptms assigned to a peptide
|
Collection<SubstitutionModification> |
getSubstitutionPTMs(Comparable proteinId,
Comparable peptideId)
Get the ptms assigned to a peptide
|
boolean |
hasPeptide()
Whether this controller contains peptides
|
boolean hasPeptide()
Collection<Comparable> getPeptideIds(Comparable proteinId)
proteinId
- identification idPeptide getPeptideByIndex(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, this can be the index of the peptide as well.int getPeptideRank(Comparable proteinId, Comparable peptideId)
proteinId
- protein idpeptideId
- peptide idCollection<String> getPeptideSequences(Comparable proteinId)
proteinId
- identification idString getPeptideSequence(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, this can be the index of the peptide as well.int getPeptideSequenceStart(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, this can be the index of the peptide as well.int getPeptideSequenceEnd(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, this can be the index of the peptide as well.Comparable getPeptideSpectrumId(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, this can be the index of the peptide as well.int getNumberOfPeptides()
int getNumberOfPeptidesByRank(int rank)
int getNumberOfPeptides(Comparable proteinId)
proteinId
- identification id.int getNumberOfUniquePeptides(Comparable proteinId)
proteinId
- identification id.int getNumberOfPTMs(Comparable proteinId)
proteinId
- identification id.int getNumberOfPTMs(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide idCollection<Modification> getPTMs(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptideint getNumberOfSubstitutionPTMs(Comparable proteinId)
proteinId
- identification id.int getNumberOfSubstitutionPTMs(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide idCollection<SubstitutionModification> getSubstitutionPTMs(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptideint getNumberOfFragmentIons(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptide as well.Collection<FragmentIon> getFragmentIons(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptide as well.Score getPeptideScore(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptide as well.Collection<PeptideEvidence> getPeptideEvidences(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptide as well.Collection<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> getAvailablePeptideLevelScores()
Integer getPeptidePrecursorCharge(Comparable identId, Comparable peptideId)
identId
- identification idpeptideId
- peptid eid, can be the index of the peptide as well.double getPeptidePrecursorMz(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptid eid, can be the index of the peptide as well.double getPeptideTheoreticalMz(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptid eid, can be the index of the peptide as well.Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.