bdbloader.cpp

来自「ncbi源码」· C++ 代码 · 共 229 行

/*
 * ===========================================================================
 * PRODUCTION $Log: bdbloader.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 19:41:28  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: bdbloader.cpp,v 1000.1 2004/06/01 19:41:28 gouriano Exp $
* ===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  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 have not placed any restriction on its use or reproduction.
*
*  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.
*
*  Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*  Author: Christiam Camacho
*
*  File Description:
*   Data loader implementation that uses the blast databases
*
* ===========================================================================
*/
#include <ncbi_pch.hpp>
#include <objtools/data_loaders/blastdb/bdbloader.hpp>
#include <objmgr/impl/handle_range_map.hpp>

#include <ctools/asn_converter.hpp>
#include <objmgr/seq_id_handle.hpp>
#include <objmgr/impl/data_source.hpp>

#include <objects/seq/Bioseq.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objmgr/util/sequence.hpp>

//=======================================================================
// BlastDbDataLoader Public interface 
// 

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)

CBlastDbDataLoader::CBlastDbDataLoader(const string& loader_name, 
        const string& dbname, const EDbType dbtype)
    : CDataLoader(loader_name), m_dbname(dbname), m_dbtype(dbtype), m_rdfp(0)
{
    m_mutex = new CFastMutex();
}

CBlastDbDataLoader::~CBlastDbDataLoader(void)
{
    if (m_rdfp) {
        CFastMutexGuard mtx(*m_mutex);
        if (m_rdfp)
            m_rdfp = readdb_destruct(m_rdfp);
    }
    delete m_mutex;
}


// TODO Note that the ranges are ignored for right now
// How to handle other choices?
void
CBlastDbDataLoader::GetRecords(const CSeq_id_Handle& idh, 
        const EChoice choice)
{
    //LOG_POST("***CBlastDbDataLoader::GetRecords***");
    // only eBioseq and eBioseqCore are supported
    switch (choice) {
        case eBlob:
        case eCore:
        case eSequence:
        case eFeatures:
        case eGraph:
        case eAll:
        default:
            LOG_POST("Invalid choice: " + NStr::IntToString(choice));
            return;
        case eBioseq:
        case eBioseqCore:
            break;
    }

    // Open the blast database if it hasn't been accessed yet
    if (!m_rdfp) {
        CFastMutexGuard mtx(*m_mutex);
        if (!m_rdfp) {
            char* tmp = strdup(m_dbname.c_str());
            m_rdfp = readdb_new_ex2(tmp, (int)m_dbtype, READDB_NEW_INDEX |
                    READDB_NEW_DO_TAXDB, NULL, NULL);
            free(tmp);
        }
    }

    // for each seqid in hrmap, look them up in db and add them to the data
    // source
    {{

        DECLARE_ASN_CONVERTER(CSeq_id, SeqId, sic);
        DECLARE_ASN_CONVERTER(CBioseq, Bioseq, bc);
        SeqIdPtr sip = NULL, sip_tmp = NULL, sip_itr = NULL, all_seqids = NULL;
        BioseqPtr bsp = NULL;
        int oid = -1;
        unsigned int index = 0;
        TOid2Bioseq::iterator found;

        CConstRef<CSeq_id> seq_id = idh.GetSeqId();
        if ( !(sip = sic.ToC(*seq_id)) )
            return;

        if ( (oid = SeqId2OrdinalId(m_rdfp, sip)) < 0)
            return;

        // If we've already retrieved this particular ordinal id, ignore it
        if ( (found = m_cache.find(oid)) != m_cache.end())
            return;

        {{  // protect access to the blast database
            CFastMutexGuard mtx(*m_mutex);
            bsp = readdb_get_bioseq(m_rdfp, oid);

            // Retrieve multiple seqids if there are any
            while (readdb_get_header(m_rdfp, oid, &index, &sip_tmp, NULL)) {
                if (!all_seqids) {
                    all_seqids = sip_tmp;
                } else {
                    sip_itr = all_seqids;
                    while (sip_itr->next)
                        sip_itr = sip_itr->next;
                    sip_itr->next = sip_tmp;
                }
            }
        }}

        if (all_seqids) {
            SeqIdSetFree(bsp->id);
            bsp->id = all_seqids;
        }

        CRef<CBioseq> bsr(bc.FromC(bsp));

        CRef<CSeq_entry> ser(new CSeq_entry());
        ser->Select(CSeq_entry::e_Seq);
        ser->SetSeq(*bsr);

        GetDataSource()->AddTSE(*ser);
        m_cache[oid] = bsr;

        bsp = BioseqFree(bsp);
        sip = SeqIdFree(sip);
    }}
}

void
CBlastDbDataLoader::DebugDump(CDebugDumpContext ddc, unsigned int depth) const
{
    //LOG_POST("CBlastDbDataLoader::DebugDump\n");
    ddc.SetFrame("CGBLoader");
    // CObject::DebugDump( ddc, depth);
    DebugDumpValue(ddc,"m_dbname", m_dbname);
    DebugDumpValue(ddc,"m_dbtype", m_dbtype);
    DebugDumpValue(ddc,"m_rdfp", m_rdfp);
}

END_SCOPE(objects)
END_NCBI_SCOPE


/* ========================================================================== 
 *
 * $Log: bdbloader.cpp,v $
 * Revision 1000.1  2004/06/01 19:41:28  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
 *
 * Revision 1.4  2004/05/21 21:42:51  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.3  2003/09/30 17:22:06  vasilche
 * Fixed for new CDataLoader interface.
 *
 * Revision 1.2  2003/09/30 16:36:36  vasilche
 * Updated CDataLoader interface.
 *
 * Revision 1.1  2003/08/06 16:15:18  jianye
 * Add BLAST DB loader.
 *
 * Revision 1.7  2003/05/19 21:11:46  camacho
 * Added caching
 *
 * Revision 1.6  2003/05/16 14:27:48  camacho
 * Proper use of namespaces
 *
 * Revision 1.5  2003/05/15 15:58:28  camacho
 * Minor changes
 *
 * Revision 1.4  2003/05/08 15:11:43  camacho
 * Changed prototype for GetRecords in base class
 *
 * Revision 1.3  2003/03/21 17:42:54  camacho
 * Added loading of taxonomy info
 *
 * Revision 1.2  2003/03/18 21:19:26  camacho
 * Retrieve all seqids if available
 *
 * Revision 1.1  2003/03/14 22:37:26  camacho
 * Initial revision
 *
 *
 * ========================================================================== */