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 Detail

      • sendAlignmentRequest

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

      • sendAlignmentRequest

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

      • isReady

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

      • getAlignmentResults

        java.io.InputStream getAlignmentResults​(java.lang.String rid,
                                        RemotePairwiseAlignmentOutputProperties out)
                                 throws java.lang.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:
        java.lang.Exception