NCBI C Toolkit Cross Reference

   /*   qblastapi.h
   * ===========================================================================
   *
   *                            PUBLIC DOMAIN NOTICE
   *            National Center for Biotechnology Information (NCBI)
   *
   *  This software/database is a "United States Government Work" under the
   *  terms of the United States Copyright Act.  It was written as part of
   *  the author's official duties as a United States Government employee and
  *  thus cannot be copyrighted.  This software/database is freely available
  *  to the public for use. The National Library of Medicine and the U.S.
  *  Government do not place any restriction on its use or reproduction.
  *  We would, however, appreciate having the NCBI and the author cited in
  *  any work or product based on this material
  *
  *  Although all reasonable efforts have been taken to ensure the accuracy
  *  and reliability of the software and data, the NLM and the U.S.
  *  Government do not and cannot warrant the performance or results that
  *  may be obtained by using this software or data. The NLM and the U.S.
  *  Government disclaim all warranties, express or implied, including
  *  warranties of performance, merchantability or fitness for any particular
  *  purpose.
  *
  * ===========================================================================
  *
  * File Name:  qblastapi.h
  *
  * Author:  Jonathan Kans
  *
  * Version Creation Date:   6/28/00
  *
  * $Revision: 1.11 $
  *
  * File Description: 
  *
  * Modifications:  
  * --------------------------------------------------------------------------
  *
  * $Log: qblastapi.h,v $
  * Revision 1.11  2003/11/03 20:51:04  madden
  * add BLASTGetBOByRIDEx
  *
  * Revision 1.10  2003/01/15 22:04:50  madden
  * Moved BLASTGetSeqAnnotByRIDEx from internal
  *
  * Revision 1.9  2003/01/02 15:06:48  boemker
  * Wrote BLASTGetQueryBioseqByRIDEx that extends behavior of
  * BLASTGetQueryBioseqByRID by returning the Bioseq for a particular query
  * (rather than always returning the Bioseq for the first query.  Modified
  * BLASTGetQueryBioseqByRID to use BLASTGetQueryBioseqByRIDEx.  Wrote
  * BLASTGetQuerySummary to return information about a query.
  *
  * Revision 1.8  2001/02/21 22:07:34  lavr
  * Changes for use new CONN interface
  *
  * Revision 1.7  2000/12/06 17:53:46  madden
  * Add prototype for QBBioseqToFasta
  *
  * Revision 1.6  2000/11/07 21:57:18  shavirin
  * Added definition of the new function BLASTGetQueryBioseqByRID()
  * Added few connection -oriented defines in the header.
  *
  * Revision 1.5  2000/07/19 15:17:15  shavirin
  * Added loging for this file.
  *
  * 
  * ==========================================================================
  */
  
  #ifndef _QBLASTAPI_
  #define _QBLASTAPI_
  
  #include <ncbi.h>
  #include <asn.h>
  #include <objseq.h>
  #include <urlquery.h>
  
  #undef NLM_EXTERN
  #ifdef NLM_IMPORT
  #define NLM_EXTERN NLM_IMPORT
  #else
  #define NLM_EXTERN extern
  #endif
  
  
  #ifdef __cplusplus
  extern "C" {
  #endif
  
  
  typedef void (LIBCALLBACK *QBlastAnnounceProc) (
    Nlm_CharPtr requestID,
    Nlm_CharPtr seqID,
    Nlm_Int2 estimatedSeconds
  );
  
  typedef Nlm_Boolean (LIBCALLBACK *QBlastResultProc) (
    Nlm_CharPtr filename,
    Nlm_VoidPtr userdata,
   Nlm_CharPtr requestID,
   Nlm_CharPtr seqID,
   Nlm_Boolean success
 );
 
 /* Opaque handle type.  Variable must be kept by application and initialized
  * to NULL.
  */
 struct QBQueueTag;
 typedef struct QBQueueTag* QBQUEUE;  /* queue handle */
 
 /* low-level connection functions */
 
 NLM_EXTERN CONN QBlastOpenConnection (
   void
 );
 
 NLM_EXTERN EIO_Status QBlastWaitForReply (
   CONN conn
 );
 
 /*
  QBlastAsynchronousRequest open a connection, send a FASTA
  request, obtains a request ID, and after the expected
  time starts checking for results every 5 seconds
 */
 
 NLM_EXTERN Boolean QBlastAsynchronousRequest (
   CharPtr database,
   CharPtr program,
   BioseqPtr bsp,
   QBQUEUE* queue,
   QBlastResultProc resultproc,
   QBlastAnnounceProc announceproc,
   VoidPtr userdata
 );
 
 /*
  QBlastCheckQueue should be called several times a
  second with a timer.  It calls QUERY_CheckQueue to
  poll connection, which calls completion routine when
  result is available, cleaning up connection afterwards.
 */
 
 NLM_EXTERN Int4 QBlastCheckQueue (
   QBQUEUE* queue
 );
 
 /*
  QBlastCheckRequest allows resumption of checking for
  a result if the program was cancelled before the result
  was ready.
 */
 
 NLM_EXTERN Boolean QBlastCheckRequest (
   CharPtr rid,
   QBQUEUE* queue,
   QBlastResultProc resultproc,
   QBlastAnnounceProc announceproc,
   VoidPtr userdata
 );
 
 /*
   Forces all connections to be closed, removes all queries from queue.
 */
 NLM_EXTERN void QBlastCloseQueue (
   QBQUEUE* queue
 );
 
 /*
   Prints a summary of active queries.
 */
 NLM_EXTERN Int4 PrintQBlastQueue (
   QBQUEUE* queue,
   FILE *fp
 );
 
 
 /* produce fasta for qblast queries. */
 Boolean QBBioseqToFasta (BioseqPtr bsp, FILE *fp, Boolean is_na);
 
 /* 
    Function to get SeqAnnot for RID. We suppose, that search already
    finished and results are exists on the Qblast repository 
 */
 NLM_EXTERN SeqAnnotPtr BLASTGetSeqAnnotByRID(CharPtr RID);
 
 /*
         Returns a SeqAnnot for a given RID.
 
         If host_machine and host_path are set to NULL and host_port to zero
         default server will be used.
 
         if query_number is set to zero all will be returned, otherwise the
         one-based offset query will be returned.
  */
 NLM_EXTERN SeqAnnotPtr BLASTGetSeqAnnotByRIDEx(CharPtr RID,
                                                Nlm_CharPtr host_machine,
                                                Nlm_Uint2 host_port,
                                                Nlm_CharPtr host_path,
                                                Int4 query_number);
 
 
 /* 
    Function to get Query Bioseq for RID. We suppose, that search already
    finished and results are exists on the Qblast repository 
 */
 NLM_EXTERN BioseqPtr BLASTGetQueryBioseqByRID(CharPtr RID);
 NLM_EXTERN BioseqPtr BLASTGetQueryBioseqByRIDEx(CharPtr RID, int query_num);
 
 NLM_EXTERN Nlm_Boolean BLASTGetQuerySummary(CharPtr RID, Int4 query_number,
     CharPtr *defline, Int4Ptr query_length);
 
 /* Function to get BlastObject for RID. We suppose, that search already
    finished and results are exists on the Qblast repository. Blast Object
    ASN.1 will be returned as CharPtr buffer
 */
 NLM_EXTERN CharPtr BLASTGetBOByRID(CharPtr RID);
 NLM_EXTERN CharPtr BLASTGetBOByRIDEx(CharPtr RID, Nlm_CharPtr host_machine, Nlm_Uint2 host_port, Nlm_CharPtr host_path);
 
 #ifdef __cplusplus
 }
 #endif
 
 #undef NLM_EXTERN
 #ifdef NLM_EXPORT
 #define NLM_EXTERN NLM_EXPORT
 #else
 #define NLM_EXTERN
 #endif
 
 #endif /* _QBLASTAPI_ */