Package psidev.psi.mi.jami.bridges.uniprot.rest

Class UniprotProteinAPIClient

java.lang.Object

psidev.psi.mi.jami.bridges.uniprot.rest.UniprotProteinAPIClient

public class UniprotProteinAPIClient
extends Object

Client for the Uniprot Protein API

Field Summary

Fields

Modifier and Type	Field	Description
static Logger	log	Sets up a logger for that class.

Constructor Summary

Constructors

Constructor	Description
UniprotProteinAPIClient()

Method Summary

Modifier and Type	Method	Description
List<String>	getSwissprotIdsForAccession(String accession, String taxonId)	Finds the list of swissProtIds for a provided ID and taxonId
List<String>	getSwissprotIdsForSequence(String sequence, String taxonId)	Finds the list of swissProtIds for a provided sequence and taxonId
List<String>	getTremblIdsForAccession(String accession, String taxonId)	Finds the list of termblIds for a provided ID and taxonId
List<String>	getTremblIdsForSequence(String sequence, String taxonId)	Finds the list of termblIds for a provided sequence and taxonId
List<Entry>	getUniparcEntries(String accession, String taxonId)	Gets the list of uniparcId matching this accession number
List<uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry>	getUniparcEntryForAccession(String accession)	Get the UniparcEntry with an accession number
String	getUniparcIdFromSequence(String sequence, String taxonId)	Gets the uniparcId matching this sequence
String[]	getUniprotBestGuessFor(String accession, String taxonId)	Get an Unique uniprot Id for this accession
List<uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry>	getUniprotEntryForAccession(String accession)	Get the UniprotEntry with its accession number
List<Entry>	getUPEntriesForAccession(String accession, String taxonId, SearchDatabase... databases)	Finds the list of UPEntries for a provided ID and organism from the provided list of databases
Entry	getUPEntriesForSequence(String sequence, String taxonId, SearchDatabase... databases)	Get the Entry which matches the sequence and taxonId in the given databases

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

log

public static final Logger log

Sets up a logger for that class.

Constructor Detail

UniprotProteinAPIClient

public UniprotProteinAPIClient()

Method Detail

getSwissprotIdsForAccession

public List<String> getSwissprotIdsForAccession(String accession,
                                                String taxonId)
                                         throws UniprotProteinAPIClientException

Finds the list of swissProtIds for a provided ID and taxonId

Parameters:

accession - the accession to look for

taxonId - the organism of the protein

Returns:

the swissprotIds if found, empty list otherwise

Throws:

UniprotProteinAPIClientException - an exception if the given accession is null

getTremblIdsForAccession

public List<String> getTremblIdsForAccession(String accession,
                                             String taxonId)
                                      throws UniprotProteinAPIClientException

Finds the list of termblIds for a provided ID and taxonId

Parameters:

accession - the accession to look for

taxonId - the organism of the protein

Returns:

the tremblId if found, empty list otherwise

Throws:

UniprotProteinAPIClientException - an exception if the given accession is null

getUniparcEntries

public List<Entry> getUniparcEntries(String accession,
                                     String taxonId)
                              throws UniprotProteinAPIClientException

Gets the list of uniparcId matching this accession number

Parameters:

accession - the accession to look for

taxonId - : the organism of the protein

Returns:

the list of uniparc Id or empty list if the accession doesn't match any Uniparc sequence

Throws:

UniprotProteinAPIClientException - an exception if the given accession is null

getUPEntriesForAccession

public List<Entry> getUPEntriesForAccession(String accession,
                                            String taxonId,
                                            SearchDatabase... databases)
                                     throws UniprotProteinAPIClientException

Finds the list of UPEntries for a provided ID and organism from the provided list of databases

Parameters:

accession - the accession to look for

taxonId - the organism of the protein

databases - the databases to query

Returns:

the uniprot ID if found, null otherwise

Throws:

UniprotProteinAPIClientException - an exception if the given accession is null

getSwissprotIdsForSequence

public List<String> getSwissprotIdsForSequence(String sequence,
                                               String taxonId)
                                        throws UniprotProteinAPIClientException

Finds the list of swissProtIds for a provided sequence and taxonId

Parameters:

sequence - the sequence to look for

taxonId - the organism of the protein

Returns:

the swissprotIds if found, empty list otherwise

Throws:

UniprotProteinAPIClientException - an exception if the given sequence is null

getTremblIdsForSequence

public List<String> getTremblIdsForSequence(String sequence,
                                            String taxonId)
                                     throws UniprotProteinAPIClientException

Finds the list of termblIds for a provided sequence and taxonId

Parameters:

sequence - the sequence to look for

taxonId - the organism of the protein

Returns:

the tremblId if found, empty list otherwise

Throws:

UniprotProteinAPIClientException - an exception if the given sequence is null

getUniparcIdFromSequence

public String getUniparcIdFromSequence(String sequence,
                                       String taxonId)
                                throws UniprotProteinAPIClientException

Gets the uniparcId matching this sequence

Parameters:

sequence - the sequence to look for

taxonId - the organism of the sequence

Returns:

the uniparc Id or null if the sequence doesn't match any Uniparc sequence

Throws:

UniprotProteinAPIClientException - an exception if the given sequence is null

getUPEntriesForSequence

public Entry getUPEntriesForSequence(String sequence,
                                     String taxonId,
                                     SearchDatabase... databases)
                              throws UniprotProteinAPIClientException

Get the Entry which matches the sequence and taxonId in the given databases

Parameters:

sequence - sequence of the protein to retrieve

taxonId - organism of the sequence

databases - the databases to look into

Returns:

an Entry instance matching the sequence, taxonId in the specific databases

Throws:

UniprotProteinAPIClientException - if the given sequence is null

getUniprotEntryForAccession

public List<uk.ac.ebi.kraken.interfaces.uniprot.UniProtEntry> getUniprotEntryForAccession(String accession)

Get the UniprotEntry with its accession number

Parameters:

accession - the Uniprot identifier of the protein we want to retrieve

Returns:

A list of UniprotEntry instances for this identifier

getUniparcEntryForAccession

public List<uk.ac.ebi.kraken.interfaces.uniparc.UniParcEntry> getUniparcEntryForAccession(String accession)

Get the UniparcEntry with an accession number

Parameters:

accession - the identifier of the protein we want to retrieve

Returns:

a list of UniparcEntry instances for this accession

getUniprotBestGuessFor

public String[] getUniprotBestGuessFor(String accession,
                                       String taxonId)
                                throws UniprotProteinAPIClientException

Get an Unique uniprot Id for this accession

Parameters:

accession - the accession to look at

taxonId - the organism

Returns:

an Unique uniprot Id

Throws:

UniprotProteinAPIClientException - if the given accession is null