Package org.biojavax.bio.alignment.blast

Class RemoteQBlastService

java.lang.Object
org.biojavax.bio.alignment.blast.RemoteQBlastService
All Implemented Interfaces:
RemotePairwiseAlignmentService
public class RemoteQBlastService extends Object implements RemotePairwiseAlignmentService
RemoteQBlastService - A simple way of submitting BLAST request to the QBlast service at NCBI.

NCBI provides a Blast server through a CGI-BIN interface. RemoteQBlastService 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 RemoteQBlastService 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. blastpgp and megablast are high-priorities.

Since:
1.8
Author:
Sylvain Foisy, Diploide BioIT

  • Constructor Details

  • Method Details

    • sendAlignmentRequest

      public String sendAlignmentRequest(String str, RemotePairwiseAlignmentProperties rpa) throws BioException
      This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a string representing the sequence. It gets the estimated time of completion by capturing the value of the RTOE variable and sets a loop that will check for completion of analysis at intervals specified by RTOE.

      It also capture the value for the RID variable, necessary for fetching the actual results after completion.

      Specified by:
      sendAlignmentRequest in interface RemotePairwiseAlignmentService
      Parameters:
      str - : a String with a sequence
      rpa - : a RemotePairwiseAlignmentProperties object
      Returns:
      rid : a String with the request ID for this sequence
      Throws:
      BioException - if it is not possible to sent the BLAST command

    • sendAlignmentRequest

      public String sendAlignmentRequest(RichSequence rs, RemotePairwiseAlignmentProperties rpa) throws BioException
      This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a RichSequence. It gets the estimated time of completion by capturing the value of the RTOE variable and sets a loop that will check for completion of analysis at intervals specified by RTOE.

      It also capture the value for the RID variable, necessary for fetching the actual results after completion.

      Specified by:
      sendAlignmentRequest in interface RemotePairwiseAlignmentService
      Parameters:
      rs - :a RichSequence object
      rpa - :a RemotePairwiseAlignmentProperties object
      Returns:
      rid : a String with the request ID for this sequence
      Throws:
      BioException - if it is not possible to sent the BLAST command

    • sendAlignmentRequest

      public String sendAlignmentRequest(int gid, RemotePairwiseAlignmentProperties rpa) throws BioException
      This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a GenBank GID. It gets the estimated time of completion by capturing the value of the RTOE variable and sets a loop that will check for completion of analysis at intervals specified by RTOE.

      It also capture the value for the RID variable, necessary for fetching the actual results after completion.

      Parameters:
      gid - :an integer with a Genbank GID
      rpa - :a RemotePairwiseAlignmentProperties object
      Returns:
      rid : a String with the request ID for this sequence
      Throws:
      BioException - if it is not possible to sent the BLAST command

    • isReady

      public boolean isReady(String id, long present) throws BioException

      This method is used only for the executeBlastSearch method to check for completion of request using the NCBI specified RTOE variable

      Specified by:
      isReady in interface RemotePairwiseAlignmentService
      Parameters:
      id - : a valid request ID
      present - : a representation of "now" using System.currentTimeMillis().
      Returns:
      a boolean value telling if the request has been completed or not.
      Throws:
      BioException - if the ID does not exist.

    • getAlignmentResults

      public InputStream getAlignmentResults(String id, RemotePairwiseAlignmentOutputProperties rb) throws BioException

      This method extracts the actual Blast report for this request ID. It uses an object implementing the RemotePairwiseAlignmentOutputProperties interface which will specify output formatting options.

      Specified by:
      getAlignmentResults in interface RemotePairwiseAlignmentService
      Parameters:
      id - :a valid request ID
      rb - : a RemotePairwiseAlignmentOutputProperties that will specify specific output formatting commands
      Returns:
      an InputStream that can be use any way one might desire
      Throws:
      BioException - if it is not possible to recover the results.

    • printRemoteBlastInfo

      public void printRemoteBlastInfo() throws BioException
      A simple method to check the availability of the QBlast service
      Throws:
      BioException - if unable to connect to the NCBI QBlast service

    • setTool

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

    • getTool

      public String getTool()
      Get the tool identifier for QBlast. Defaults to 'biojavax'.
      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.