bl2seq.cpp

ncbi源码

{
    mi_pResults = NULL;
    mi_pDiagnostics = Blast_DiagnosticsInit();

    Blast_HSPResultsInit(mi_clsQueryInfo->num_queries, &mi_pResults);

    BLAST_SearchEngine(m_OptsHandle->GetOptions().GetProgram(),
                       mi_clsQueries, mi_clsQueryInfo, 
                       mi_pSeqSrc, mi_pScoreBlock, 
                       m_OptsHandle->GetOptions().GetScoringOpts(),
                       mi_pLookupTable,
                       m_OptsHandle->GetOptions().GetInitWordOpts(),
                       m_OptsHandle->GetOptions().GetExtnOpts(),
                       m_OptsHandle->GetOptions().GetHitSaveOpts(),
                       m_OptsHandle->GetOptions().GetEffLenOpts(),
                       NULL, m_OptsHandle->GetOptions().GetDbOpts(),
                       mi_pResults, mi_pDiagnostics);
}

/** Unlike the database search, we want to make sure that a seqalign list is   
 * returned for each query/subject pair, even if it is empty. Also we don't 
 * want subjects to be sorted in seqalign results. Hence we retrieve results 
 * for each subject separately and append the resulting vectors of seqalign
 * lists. 
 */
TSeqAlignVector
CBl2Seq::x_Results2SeqAlign()
{
    TSeqAlignVector retval;
    retval.reserve(m_tQueries.size());

    ASSERT(mi_pResults->num_queries == (int)m_tQueries.size());

    for (unsigned int index = 0; index < m_tSubjects.size(); ++index)
    {
        TSeqAlignVector seqalign =
            BLAST_OneSubjectResults2CSeqAlign(mi_pResults,
                 m_OptsHandle->GetOptions().GetProgram(),
                 m_tQueries, mi_pSeqSrc, index,
                 m_OptsHandle->GetOptions().GetScoringOpts(), 
                 mi_pScoreBlock);

        /* Merge the new vector with the current. Assume that both vectors
           contain CSeq_align_sets for all queries, i.e. have the same 
           size. */
        ASSERT(seqalign.size() == m_tQueries.size());

        if (retval.size() == 0) {
            // First time around, just fill the empty vector with the 
            // seqaligns from the first subject.
            retval.swap(seqalign);
        } else {

            for (unsigned int i = 0; i < retval.size(); ++i) {
                retval[i]->Set().splice(retval[i]->Set().end(),
                                       seqalign[i]->Set());
            }

        }
    }

    // Clean up structures
    mi_clsInitWordParams.Reset(NULL);
    mi_clsHitSavingParams.Reset(NULL);
    mi_clsExtnWord.Reset(NULL);
    mi_clsExtnParams.Reset(NULL);
    mi_clsGapAlign.Reset(NULL);

    return retval;
}

END_SCOPE(blast)
END_NCBI_SCOPE

/* @} */

/*
 * ===========================================================================
 *
 * $Log: bl2seq.cpp,v $
 * Revision 1000.4  2004/06/01 18:05:35  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.53
 *
 * Revision 1.53  2004/05/21 21:41:02  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.52  2004/05/14 17:16:12  dondosha
 * BlastReturnStat structure changed to BlastDiagnostics and refactored
 *
 * Revision 1.51  2004/05/07 15:28:05  papadopo
 * add scale factor of 1.0 to BlastMainSetup
 *
 * Revision 1.50  2004/05/05 15:28:56  dondosha
 * Renamed functions in blast_hits.h accordance with new convention Blast_[StructName][Task]
 *
 * Revision 1.49  2004/04/30 16:53:06  dondosha
 * Changed a number of function names to have the same conventional Blast_ prefix
 *
 * Revision 1.48  2004/04/05 16:09:27  camacho
 * Rename DoubleInt -> SSeqRange
 *
 * Revision 1.47  2004/03/24 19:14:48  dondosha
 * Fixed memory leaks
 *
 * Revision 1.46  2004/03/19 19:22:55  camacho
 * Move to doxygen group AlgoBlast, add missing CVS logs at EOF
 *
 * Revision 1.45  2004/03/15 19:56:03  dondosha
 * Use sequence source instead of accessing subjects directly
 *
 * Revision 1.44  2004/03/10 17:37:36  papadopo
 * add (unused) RPS info pointer to LookupTableWrapInit()
 *
 * Revision 1.43  2004/02/24 18:16:29  dondosha
 * Removed lookup options argument from call to BLAST_MainSetUp
 *
 * Revision 1.42  2004/02/13 21:21:30  camacho
 * Add throws clause to Run method
 *
 * Revision 1.41  2004/02/13 19:32:55  camacho
 * Removed unnecessary #defines
 *
 * Revision 1.40  2004/01/16 21:52:59  bealer
 * - Changes for Blast4 API
 *
 * Revision 1.39  2004/01/02 18:53:27  camacho
 * Fix assertion
 *
 * Revision 1.38  2003/12/03 16:43:46  dondosha
 * Renamed BlastMask to BlastMaskLoc, BlastResults to BlastHSPResults
 *
 * Revision 1.37  2003/11/26 18:23:58  camacho
 * +Blast Option Handle classes
 *
 * Revision 1.36  2003/11/03 15:20:39  camacho
 * Make multiple query processing the default for Run().
 *
 * Revision 1.35  2003/10/31 00:05:15  camacho
 * Changes to return discontinuous seq-aligns for each query-subject pair
 *
 * Revision 1.34  2003/10/30 19:34:53  dondosha
 * Removed gapped_calculation from BlastHitSavingOptions structure
 *
 * Revision 1.33  2003/09/11 17:45:03  camacho
 * Changed CBlastOption -> CBlastOptions
 *
 * Revision 1.32  2003/09/10 20:01:30  dondosha
 * Use lookup_wrap.h
 *
 * Revision 1.31  2003/09/09 20:31:13  camacho
 * Add const type qualifier
 *
 * Revision 1.30  2003/09/09 15:18:02  camacho
 * Fix includes
 *
 * Revision 1.29  2003/09/09 12:55:09  camacho
 * Moved setup member functions to blast_setup_cxx.cpp
 *
 * Revision 1.28  2003/09/03 19:36:58  camacho
 * Fix include path for blast_setup.hpp, code clean up
 *
 * Revision 1.27  2003/08/28 22:42:54  camacho
 * Change BLASTGetSequence signature
 *
 * Revision 1.26  2003/08/28 17:37:06  camacho
 * Fix memory leaks, properly reset structure wrappers
 *
 * Revision 1.25  2003/08/28 15:48:23  madden
 * Make buf one longer for sentinel byte
 *
 * Revision 1.24  2003/08/25 17:15:49  camacho
 * Removed redundant typedef
 *
 * Revision 1.23  2003/08/19 22:12:47  dondosha
 * Cosmetic changes
 *
 * Revision 1.22  2003/08/19 20:27:06  dondosha
 * EProgram enum type is no longer part of CBlastOptions class
 *
 * Revision 1.21  2003/08/19 13:46:13  dicuccio
 * Added 'USING_SCOPE(objects)' to .cpp files for ease of reading implementation.
 *
 * Revision 1.20  2003/08/18 22:17:36  camacho
 * Renaming of SSeqLoc members
 *
 * Revision 1.19  2003/08/18 20:58:57  camacho
 * Added blast namespace, removed *__.hpp includes
 *
 * Revision 1.18  2003/08/18 19:58:50  dicuccio
 * Fixed compilation errors after change from pair<> to SSeqLoc
 *
 * Revision 1.17  2003/08/18 17:07:41  camacho
 * Introduce new SSeqLoc structure (replaces pair<CSeq_loc, CScope>).
 * Change in function to read seqlocs from files.
 *
 * Revision 1.16  2003/08/15 15:59:13  dondosha
 * Changed call to BLAST_Results2CSeqAlign according to new prototype
 *
 * Revision 1.15  2003/08/12 19:21:08  dondosha
 * Subject id argument to BLAST_Results2CppSeqAlign is now a simple pointer, allowing it to be NULL
 *
 * Revision 1.14  2003/08/11 19:55:55  camacho
 * Early commit to support query concatenation and the use of multiple scopes.
 * Compiles, but still needs work.
 *
 * Revision 1.13  2003/08/11 15:23:59  dondosha
 * Renamed conversion functions between BlastMaskLoc and CSeqLoc; added algo/blast/core to headers from core BLAST library
 *
 * Revision 1.12  2003/08/11 14:00:41  dicuccio
 * Indenting changes.  Fixed use of C++ namespaces (USING_SCOPE(objects) inside of
 * BEGIN_NCBI_SCOPE block)
 *
 * Revision 1.11  2003/08/08 19:43:07  dicuccio
 * Compilation fixes: #include file rearrangement; fixed use of 'list' and
 * 'vector' as variable names; fixed missing ostrea<< for __int64
 *
 * Revision 1.10  2003/08/01 17:40:56  dondosha
 * Use renamed functions and structures from local blastkar.h
 *
 * Revision 1.9  2003/07/31 19:45:33  camacho
 * Eliminate Ptr notation
 *
 * Revision 1.8  2003/07/30 19:58:02  coulouri
 * use ListNode
 *
 * Revision 1.7  2003/07/30 15:00:01  camacho
 * Do not use Malloc/MemNew/MemFree
 *
 * Revision 1.6  2003/07/29 14:15:12  camacho
 * Do not use MemFree/Malloc
 *
 * Revision 1.5  2003/07/28 22:20:17  camacho
 * Removed unused argument
 *
 * Revision 1.4  2003/07/23 21:30:40  camacho
 * Calls to options member functions
 *
 * Revision 1.3  2003/07/15 19:21:36  camacho
 * Use correct strands and sequence buffer length
 *
 * Revision 1.2  2003/07/14 22:16:37  camacho
 * Added interface to retrieve masked regions
 *
 * Revision 1.1  2003/07/10 18:34:19  camacho
 * Initial revision
 *
 *
 * ===========================================================================
 */