public interface QuantDataAccess
Modifier and Type | Method and Description |
---|---|
Collection<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> |
getAvailableQuantPeptideLevelScores()
Get a collection of peptide scores in cv term reference format
|
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
|
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 |
getNumberOfUniqueQuantPeptides(Comparable proteinId)
Get the number of unique peptides of a 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
|
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
|
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
|
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
|
Map<Comparable,StudyVariable> |
getStudyVariables()
In mzTab files the information of Quantitation is store in StudyVariables and not in Samples
|
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 |
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 |
hasProteinQuantData()
Check whether the experiment contains quantitative data at the protein level
|
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 hasQuantData()
boolean hasProteinQuantData()
boolean hasProteinTotalIntensities()
boolean hasPeptideQuantData()
boolean hasPeptideTotalIntensities()
boolean hasLabelFreeQuantMethods()
Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> getLabelFreeQuantMethods()
Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> getProteinLabelFreeQuantMethods()
Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> getPeptideLabelFreeQuantMethods()
boolean hasIsotopeLabellingQuantMethods()
Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> getProteinIsotopeLabellingQuantMethods()
Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> getPeptideIsotopeLabellingQuantMethods()
Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> getIsotopeLabellingQuantMethods()
Collection<uk.ac.ebi.pride.utilities.term.QuantCvTermReference> getQuantMethods()
int getNumberOfReagents()
int getReferenceSubSampleIndex()
QuantitativeSample getQuantSample()
uk.ac.ebi.pride.utilities.term.QuantCvTermReference getProteinQuantUnit()
uk.ac.ebi.pride.utilities.term.QuantCvTermReference getPeptideQuantUnit()
Quantification getProteinQuantData(Comparable proteinId)
proteinId
- protein identification idQuantification getPeptideQuantData(Comparable proteinId, Comparable peptideId)
proteinId
- protein identification idpeptideId
- peptide idMap<Comparable,StudyVariable> getStudyVariables()
QuantScore getProteinQuantStudyData(Comparable proteinId)
proteinId
- Protein IDQuantScore getPeptideQuantStudyData(Comparable proteinID, Comparable peptideId)
proteinID
- Protein IdentifierpeptideId
- Peptide Identifierboolean hasQuantPeptide()
Collection<Comparable> getQuantPeptideIds(Comparable proteinId)
proteinId
- identification idQuantPeptide getQuantPeptideByIndex(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, this can be the index of the peptide as well.Collection<String> getQuantPeptideSequences(Comparable proteinId)
proteinId
- identification idString getQuantPeptideSequence(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, this can be the index of the peptide as well.Comparable getQuantPeptideSpectrumId(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, this can be the index of the peptide as well.int getNumberOfQuantPeptides()
int getNumberOfQuantPeptides(Comparable proteinId)
proteinId
- identification id.int getNumberOfUniqueQuantPeptides(Comparable proteinId)
proteinId
- identification id.int getNumberOfQuantPTMs(Comparable proteinId)
proteinId
- identification id.int getNumberOfQuantPTMs(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide idCollection<Modification> getQuantPTMs(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptideScore getQuantPeptideScore(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptide as well.QuantScore getQuantPeptideQuantScore(Comparable proteinId, Comparable peptideId)
proteinId
- identification idpeptideId
- peptide id, can be the index of the peptide as well.Collection<PeptideEvidence> getQuantPeptideEvidences(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> getAvailableQuantPeptideLevelScores()
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