Package org.biojavax.bio.alignment

Interface RemotePairwiseAlignmentService

All Known Implementing Classes:

RemoteQBlastService

public interface RemotePairwiseAlignmentService

This interface specifies minimal information needed to execute a pairwise alignment on a remote service. Example of service: QBlast service at NCBI Web Service at EBI

Since:

1.8

Author:

Sylvain Foisy

Method Summary

Modifier and Type	Method	Description
InputStream	getAlignmentResults(String rid, RemotePairwiseAlignmentOutputProperties out)	Getting the actual alignment results from this instantiated service for a given ID with specific formatting parameters held in a RemotePairwiseAlignmentOutputProperties-implemented object.
boolean	isReady(String id, long present)	Simple method to check if the specified request has been completed by the service used.
String	sendAlignmentRequest(String str, RemotePairwiseAlignmentProperties rpa)	Doing the actual analysis on the instantiated service using specified parameters on the string representation of the Sequence object
String	sendAlignmentRequest(RichSequence rs, RemotePairwiseAlignmentProperties rpa)	Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object

Method Detail

sendAlignmentRequest

String sendAlignmentRequest(RichSequence rs,
                            RemotePairwiseAlignmentProperties rpa)
                     throws BioException

Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object

Throws:

BioException

sendAlignmentRequest

String sendAlignmentRequest(String str,
                            RemotePairwiseAlignmentProperties rpa)
                     throws BioException

Doing the actual analysis on the instantiated service using specified parameters on the string representation of the Sequence object

Throws:

BioException

isReady

boolean isReady(String id,
                long present)
         throws BioException

Simple method to check if the specified request has been completed by the service used.

Parameters:

id - :an ID for an alignment request

present - :a long integer value representing the actual time

Returns:

a boolean value telling if this requestID has been completed or not.

Throws:

BioException - if the ID does not exist.

getAlignmentResults

InputStream getAlignmentResults(String rid,
                                RemotePairwiseAlignmentOutputProperties out)
                         throws BioException

Getting the actual alignment results from this instantiated service for a given ID with specific formatting parameters held in a RemotePairwiseAlignmentOutputProperties-implemented object.

Parameters:

rid - :a String with the request ID for this single alignment run

out - :a RemotePairwiseAlignmentOutputProperties with the specific output instructions.

Returns:

: an InputStream with the actual alignment results

Throws:

BioException