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
 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(RichSequence rs, RemotePairwiseAlignmentProperties rpa)
          Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object
 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
 

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


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