Package org.biojava.nbio.ws.alignment.qblast

Class NCBIQBlastService

java.lang.Object
org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService
All Implemented Interfaces:
RemotePairwiseAlignmentService
public class NCBIQBlastService extends Object implements RemotePairwiseAlignmentService
Provides a simple way of submitting BLAST request to the QBlast service at NCBI.

NCBI provides a Blast server through a CGI-BIN interface. This service simply encapsulates an access to it by giving users access to get/set methods to fix sequence, program and database as well as advanced options.

The philosophy behind this service is to disconnect submission of Blast requests from collection of Blast results. This is done so to allow a user to submit multiple Blast requests while allowing recovery of the reports at a later time.

Presently, only blastall programs are accessible.

Author:
Sylvain Foisy, Diploide BioIT, Gediminas Rimsa

  • Field Details

    • WAIT_INCREMENT

      public static final long WAIT_INCREMENT
      Number of milliseconds by which expected job execution time is incremented if it is not finished yet. Subsequent calls to isReady(String, long) method will return false until at least this much time passes.
      See Also:

  • Constructor Details

    • NCBIQBlastService

      public NCBIQBlastService()
      Constructs a service object that targets the public NCBI BLAST network service.

    • NCBIQBlastService

      public NCBIQBlastService(String svcUrl)
      Constructs a service object which targets a custom NCBI BLAST network service (e.g.: an instance of BLAST in the cloud).
      Parameters:
      svcUrl - : a String containing the base URL to send requests to, e.g.: http://host.my.cloud.service.provider.com/cgi-bin/blast.cgi
      See Also:

  • Method Details

    • getRemoteBlastInfo

      public String getRemoteBlastInfo() throws Exception
      A simple method to check the availability of the QBlast service. Sends Info command to QBlast
      Returns:
      QBlast info output concatenated to String
      Throws:
      Exception - if unable to connect to the NCBI QBlast service

    • sendAlignmentRequest

      public String sendAlignmentRequest(Sequence<Compound> seq, RemotePairwiseAlignmentProperties rpa) throws Exception
      Converts given sequence to String and calls sendAlignmentRequest(String, RemotePairwiseAlignmentProperties)
      Specified by:
      sendAlignmentRequest in interface RemotePairwiseAlignmentService
      Throws:
      Exception

    • sendAlignmentRequest

      public String sendAlignmentRequest(int gid, RemotePairwiseAlignmentProperties rpa) throws Exception
      Converts given GenBank GID to String and calls sendAlignmentRequest(String, RemotePairwiseAlignmentProperties)
      Throws:
      Exception

    • sendAlignmentRequest

      public String sendAlignmentRequest(String query, RemotePairwiseAlignmentProperties alignmentProperties) throws Exception
      Sends the Blast request via the Put command of the CGI-BIN interface. Uses all of the parameters specified in alignmentProperties (parameters PROGRAM and DATABASE are required).
      Specified by:
      sendAlignmentRequest in interface RemotePairwiseAlignmentService
      Parameters:
      query - : a String representing a sequence or Genbank ID
      alignmentProperties - : a RemotePairwiseAlignmentProperties object representing alignment properties
      Returns:
      the request id for this sequence, necessary to fetch results after completion
      Throws:
      Exception - if unable to connect to the NCBI QBlast service or if no sequence or required parameters PROGRAM and DATABASE are not set

    • isReady

      public boolean isReady(String id) throws Exception
      Wrapper method for isReady(String, long), omitting unnecessary present property.
      Throws:
      Exception
      See Also:

    • isReady

      public boolean isReady(String id, long present) throws Exception
      Checks for completion of request.

      If expected execution time (RTOE) is available for request, this method will always return false until that time passes. This is done to prevent sending unnecessary requests to the server.

      Specified by:
      isReady in interface RemotePairwiseAlignmentService
      Parameters:
      id - : request id, which was returned by sendAlignmentRequest method
      present - : is not used, can be any value
      Returns:
      a boolean value telling if the request has been completed
      Throws:
      Exception - if the ID does not exist.

    • getAlignmentResults

      public InputStream getAlignmentResults(String id, RemotePairwiseAlignmentOutputProperties outputProperties) throws Exception
      Extracts the actual Blast report for given request id according to options provided in outputProperties argument.

      If the results are not ready yet, sleeps until they are available. If sleeping is not desired, call this method after isReady returns true

      Specified by:
      getAlignmentResults in interface RemotePairwiseAlignmentService
      Parameters:
      id - : request id, which was returned by sendAlignmentRequest method
      outputProperties - : an object specifying output formatting options
      Returns:
      an InputStream of results
      Throws:
      Exception - if it is not possible to recover the results

    • sendDeleteRequest

      public void sendDeleteRequest(String id)
      Sends a delete request for given request id. Optional operation, ignores IOExceptions.
      Can be used after results of given search are no longer needed to be kept on Blast server
      Parameters:
      id - request id, as returned by sendAlignmentRequest method

    • setTool

      public void setTool(String tool)
      Set the tool identifier for QBlast. Defaults to "biojava5"
      Parameters:
      tool - the new identifier

    • getTool

      public String getTool()
      Get the tool identifier for QBlast. Defaults to "biojava5"
      Returns:
      the identifier

    • setEmail

      public void setEmail(String email)
      Set the email for QBlast. Defaults to "anonymous@biojava.org"
      Parameters:
      email - the new email

    • getEmail

      public String getEmail()
      Get the email for QBlast. Defaults to "anonymous@biojava.org".
      Returns:
      the email