Package org.biojava.nbio.ws.alignment

Interface RemotePairwiseAlignmentService

All Known Implementing Classes:
NCBIQBlastService
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:
Biojava 3
Author:
Sylvain Foisy

  • Method Details

    • sendAlignmentRequest

      String sendAlignmentRequest(Sequence<Compound> seq, RemotePairwiseAlignmentProperties rpa) throws Exception
      Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object
      Throws:
      Exception

    • sendAlignmentRequest

      String sendAlignmentRequest(String str, RemotePairwiseAlignmentProperties rpa) throws Exception
      Doing the actual analysis on the instantiated service using specified parameters on the string representation of the Sequence object
      Throws:
      Exception

    • isReady

      boolean isReady(String id, long present) throws Exception
      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:
      Exception - if the ID does not exist.

    • getAlignmentResults

      InputStream getAlignmentResults(String rid, RemotePairwiseAlignmentOutputProperties out) throws Exception
      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:
      Exception