Package psidev.psi.mi.jami.bridges.unisave

Class UnisaveClient

java.lang.Object

psidev.psi.mi.jami.bridges.unisave.UnisaveClient

All Implemented Interfaces:

SequenceVersionFetcher

public class UnisaveClient
extends Object
implements SequenceVersionFetcher

Client to query unisave and collect sequence versions or sequence from a particular version

Since:

30/09/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
UnisaveClient()	Constructor for UnisaveClient.

Method Summary

Modifier and Type	Method	Description
String	fetchSequenceFromVersion(String id, int version)	fetchSequenceFromVersion.
int	fetchVersionFromSequence(String id, String sequence)	fetchVersionFromSequence.
Map<Integer,String>	getAllSequencesBeforeDate(String identifier, Date date)	Get the map of sequences (and their sequence version in uniprot) existing in unisave before this date
List<SequenceVersion>	getAvailableSequenceUpdate(String identifier, String sequence)	Collects all available sequence update fro mUniSave.
int	getConnectionTimeOut()	Getter for the field connectionTimeOut.
FastaSequence	getFastaSequence(String identifier, int version)	Retrieve a fasta sequence corresponding to a given EntryVersion.
String	getLastSequenceAtTheDate(String identifier, Date date)	getLastSequenceAtTheDate.
String	getSequenceFor(String identifier, int sequence_version)	getSequenceFor.
int	getSequenceVersion(String identifier, String sequence)	Returns the sequence version of a sequence for a certain uniprot ac.
int	getSocketTimeout()	Getter for the field socketTimeout.
List<Integer>	getVersions(String identifier)	Searches for all entry version given its identifier.
void	setConnectionTimeOut(int connectionTimeOut)	Setter for the field connectionTimeOut.
void	setSocketTimeout(int socketTimeout)	Setter for the field socketTimeout.

Methods inherited from class java.lang.Object

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

Constructor Detail

UnisaveClient

public UnisaveClient()

Constructor for UnisaveClient.

Method Detail

getSequenceFor

public String getSequenceFor(String identifier,
                             int sequence_version)
                      throws BridgeFailedException

getSequenceFor.

Parameters:

identifier - a String object.

sequence_version - a int.

Returns:

a String object.

Throws:

BridgeFailedException - if any.

getVersions

public List<Integer> getVersions(String identifier)
                          throws BridgeFailedException

Searches for all entry version given its identifier.

Parameters:

identifier - the identifier of the entry we are interested in.

Returns:

list of all versions of the given entry from the most recent to the oldest.

Throws:

BridgeFailedException - if the identifier cannot be found in UniSave.

getLastSequenceAtTheDate

public String getLastSequenceAtTheDate(String identifier,
                                       Date date)
                                throws BridgeFailedException

getLastSequenceAtTheDate.

Parameters:

identifier - a String object.

date - a Date object.

Returns:

a String object.

Throws:

BridgeFailedException - if any.

getAllSequencesBeforeDate

public Map<Integer,String> getAllSequencesBeforeDate(String identifier,
                                                           Date date)
                                                    throws BridgeFailedException

Get the map of sequences (and their sequence version in uniprot) existing in unisave before this date

Parameters:

identifier - a String object.

date - a Date object.

Returns:

a Map object.

Throws:

BridgeFailedException - if any.

getFastaSequence

public FastaSequence getFastaSequence(String identifier,
                                      int version)
                               throws BridgeFailedException

Retrieve a fasta sequence corresponding to a given EntryVersion.

Parameters:

version - the version for which we want the sequence

identifier - a String object.

Returns:

a fasta sequence.

Throws:

BridgeFailedException - if the version given doesn't have an entryId that can be found in UniSave.

getSequenceVersion

public int getSequenceVersion(String identifier,
                              String sequence)
                       throws BridgeFailedException

Returns the sequence version of a sequence for a certain uniprot ac. Returns -1 if the sequence cannot be found for this uniprot ac

Parameters:

identifier - a String object.

sequence - a String object.

Returns:

a int.

Throws:

BridgeFailedException - if any.

getAvailableSequenceUpdate

public List<SequenceVersion> getAvailableSequenceUpdate(String identifier,
                                                        String sequence)
                                                 throws BridgeFailedException

Collects all available sequence update fro mUniSave.

Parameters:

identifier - identifier of the uniprot entry

sequence - sequence for which we want the subsequent updates

Returns:

a non null ordered list. If the given sequence is found in the entry history, this sequence at least is returned. If there were say, 2 updates since that protein sequence, the list would contain 3 versions. If we fail to find a match for the given sequence in UniSave, the list would contain all existing sequence update available. The list of ordered from the oldest to the most recent sequence.

Throws:

BridgeFailedException - if the identifier cannot be found in UniSave.

fetchSequenceFromVersion

public String fetchSequenceFromVersion(String id,
                                       int version)
                                throws BridgeFailedException

fetchSequenceFromVersion.

Specified by:

fetchSequenceFromVersion in interface SequenceVersionFetcher

Parameters:

id - a String object.

version - a int.

Returns:

a String object.

Throws:

BridgeFailedException - if any.

fetchVersionFromSequence

public int fetchVersionFromSequence(String id,
                                    String sequence)
                             throws BridgeFailedException

fetchVersionFromSequence.

Specified by:

fetchVersionFromSequence in interface SequenceVersionFetcher

Parameters:

id - a String object.

sequence - a String object.

Returns:

a int.

Throws:

BridgeFailedException - if any.

getSocketTimeout

public int getSocketTimeout()

Getter for the field socketTimeout.

Returns:

a int.

setSocketTimeout

public void setSocketTimeout(int socketTimeout)

Setter for the field socketTimeout.

Parameters:

socketTimeout - a int.

getConnectionTimeOut

public int getConnectionTimeOut()

Getter for the field connectionTimeOut.

Returns:

a int.

setConnectionTimeOut

public void setConnectionTimeOut(int connectionTimeOut)

Setter for the field connectionTimeOut.

Parameters:

connectionTimeOut - a int.