public interface ProteinDataAccess
Modifier and Type | Method and Description |
---|---|
Collection<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> |
getAvailableProteinLevelScores()
get a list of present protein scores in CV terms
|
int |
getNumberOfProteins()
Get the total number of protein identifications.
|
String |
getProteinAccession(Comparable proteinId)
Get the protein accession of a identification
|
String |
getProteinAccessionVersion(Comparable proteinId)
Get the protein accession version of a identification
|
Protein |
getProteinById(Comparable proteinId)
Get a Identification object
|
double |
getProteinCoverage(Comparable proteinId)
This function returns the protein coverage for a protein
|
Collection<Comparable> |
getProteinIds()
Get a collection of identification ids
|
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.
|
SearchDataBase |
getSearchDatabase(Comparable proteinId)
Get the search database of a identification
|
String |
getSearchDatabaseVersion(Comparable proteinId)
Get the search database version of a identification
|
Collection<uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference> |
getSearchEngineCvTermReferences()
Get the search engine of a identification
|
boolean |
hasDecoyInformation()
This function return true if the controller contains decoy information and false if the controller do not contain decoy information.
|
boolean |
hasProtein()
Whether this controller contains identifications
|
boolean |
hasProteinSequence()
Whether this controller contains protein sequences
|
int |
indexOfProtein(Comparable proteinId)
Get the index of identification by its id
|
boolean hasProtein()
Collection<Comparable> getProteinIds()
int indexOfProtein(Comparable proteinId)
proteinId
- identification idProtein getProteinById(Comparable proteinId)
proteinId
- a string id of Identificationint getNumberOfProteins()
String getProteinAccession(Comparable proteinId)
proteinId
- identification id.String getProteinAccessionVersion(Comparable proteinId)
proteinId
- identification id.double getProteinScore(Comparable proteinId)
proteinId
- identification id.double getProteinCoverage(Comparable proteinId)
proteinId
- Protein IdScore getProteinScores(Comparable proteinId)
proteinId
- Protein Iddouble getProteinThreshold(Comparable proteinId)
proteinId
- identification id.SearchDataBase getSearchDatabase(Comparable proteinId)
proteinId
- identification id.Collection<uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference> getSearchEngineCvTermReferences()
String getSearchDatabaseVersion(Comparable proteinId)
proteinId
- identification idCollection<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> getAvailableProteinLevelScores()
DBSequence getProteinSequence(Comparable proteinId)
proteinId
- identification Idboolean hasProteinSequence()
boolean hasDecoyInformation()
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