blast_base.cpp

来自「ncbi源码」· C++ 代码 · 共 304 行

/*
 * ===========================================================================
 * PRODUCTION $Log: blast_base.cpp,v $
 * PRODUCTION Revision 1000.5  2004/06/01 20:54:12  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.10
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: blast_base.cpp,v 1000.5 2004/06/01 20:54:12 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.
 *
 * ===========================================================================
 *
 * Authors:  Mike DiCuccio
 *
 * File Description:
 *
 */

#include <ncbi_pch.hpp>
#include "blast_base.hpp"
#include "blast_util.hpp"

#include <gui/core/doc_manager.hpp>
#include <gui/plugin/PluginInfo.hpp>
#include <gui/plugin/PluginCommandSet.hpp>
#include <gui/plugin/PluginCommand.hpp>
#include <gui/plugin/PluginRequest.hpp>
#include <gui/plugin/PluginArgSet.hpp>
#include <gui/core/version.hpp>
#include <gui/utils/message_box.hpp>
#include <gui/core/plugin_utils.hpp>

#include <algo/blast/api/bl2seq.hpp>
#include <algo/blast/api/blast_options.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Seq_align.hpp>

#include <serial/serial.hpp>
#include <serial/objostrasn.hpp>

BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


//
// utility function for translating between plugin arg loc-lists
// and BLAST loc vectors
//
inline
blast::TSeqLocVector x_ToBlastVec(const plugin_args::TLocList& locs)
{
    blast::SSeqLoc loc;
    blast::TSeqLocVector vec;
    vec.reserve(locs.size());

    ITERATE (plugin_args::TLocList, iter, locs) {
        loc.seqloc = iter->second;
        loc.scope = &(iter->first->GetScope());

        vec.push_back(loc);
    }

    return vec;
}



// standard info boilerplate
void CAlgoBlast_Base::x_AddStandardArgs(CPluginCommand& command)
{
}


void CAlgoBlast_Base::RunCommand(CPluginMessage& msg)
{
    const CPluginCommand& cmd   = msg.GetRequest().GetCommand();
    CPluginReply&         reply = msg.SetReply();
    //
    // retrieve our query sequences
    //
    plugin_args::TLocList query;
    GetArgValue(cmd["query"], query);

    //
    // retrieve our target sequences
    //
    plugin_args::TLocList targets;
    GetArgValue(cmd["targets"], targets);

    //
    // compose the query and target sequences into BLAST forms
    //
    blast::TSeqLocVector query_vec  = x_ToBlastVec(query);
    blast::TSeqLocVector target_vec = x_ToBlastVec(targets);

    //
    // retrieve the program type we're running
    //
    string prog_name = cmd["prog"].AsString();

    //
    // switch based on the program
    //
    CRef<CSeq_annot> annot(new CSeq_annot());
    if ( !annot ) {
        reply.SetStatus(eMessageStatus_failed);
        return;
    }
    blast::EProgram prog = blast::eBlastn;

    if (prog_name == "blastn") {
        annot->AddTitle("BLASTn Output");
        prog = blast::eBlastn;
    } else if (prog_name == "blastp") {
        annot->AddTitle("BLASTp Output");
        prog = blast::eBlastp;
    } else if (prog_name == "blastx") {
        annot->AddTitle("BLASTx Output");
        prog = blast::eBlastx;
    } else {
        annot->AddTitle("tBLASTx Output");
        prog = blast::eTblastx;
    }

    //
    // parse our options
    //
    blast::CBl2Seq blaster(query_vec, target_vec, prog);
    CBlastUtils::ArgsToBlastOptions(cmd, blaster.SetOptions());

    //
    // blast!
    //
    // run blast
	blast::TSeqAlignVector aligns = blaster.Run();

    // make an annotation
	ITERATE (blast::TSeqAlignVector, iter, aligns) {
        ITERATE (CSeq_align_set::Tdata, align_iter, (*iter)->Get()) {
            if ((*align_iter)->GetSegs().IsDisc()) {
                annot->SetData().SetAlign()
                    .insert(annot->SetData().SetAlign().end(),
                            (*align_iter)->GetSegs().GetDisc().Get().begin(),
                            (*align_iter)->GetSegs().GetDisc().Get().end());
            } else {
                annot->SetData().SetAlign().push_back(*align_iter);
            }
        }
	}

    _TRACE("CAlgoBlastBase: found " << annot->GetData().GetAlign().size()
           << " alignments");

    if (annot->GetData().GetAlign().size() == 0) {
        NcbiMessageBox("No alignments found.");
        return;
    }

    //
    // pass back to the system.  We may use the same scope and just attach,
    // if that is appropriate
    //
    CConstRef<IDocument> doc_ref;

    ITERATE (plugin_args::TLocList, iter, query) {
        if ( !doc_ref ) {
            doc_ref.Reset(iter->first);
        } else if (iter->first != doc_ref) {
            doc_ref.Reset();
            break;
        }
    }

    if (doc_ref) {
        ITERATE (plugin_args::TLocList, iter, targets) {
            if (iter->second != doc_ref) {
                doc_ref.Reset();
                break;
            }
        }
    }

    //
    // create a new document and launch a viewer for our alignment
    //
    if ( !doc_ref ) {
        //
        // query and targets come from different documents
        // create a new one to handle the results
        //
        CRef<CScope> new_scope(new CScope(CDocManager::GetObjectManager()));
        ITERATE (plugin_args::TLocList, iter, query) {
            new_scope->AddScope(iter->first->GetScope());
        }
        ITERATE (plugin_args::TLocList, iter, targets) {
            new_scope->AddScope(iter->first->GetScope());
        }

        doc_ref.Reset(CDocManager::CreateDocument(*new_scope, *annot));
    }

    CRef<CSelectionBuffer> buf(new CSelectionBuffer());
    buf->AddSelection(doc_ref, *annot);
    CPluginUtils::CallPlugin("CAlnMultiView",
                             eViewCommand_new_view, *buf);
    reply.AddAction(CPluginReplyAction::e_Add_to_document);
    reply.AddObject(*doc_ref, *annot);
    reply.SetStatus(eMessageStatus_success);
}


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: blast_base.cpp,v $
 * Revision 1000.5  2004/06/01 20:54:12  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.10
 *
 * Revision 1.10  2004/05/21 22:27:46  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.9  2004/04/07 12:51:48  dicuccio
 * Removed dead code
 *
 * Revision 1.8  2004/01/27 18:40:04  dicuccio
 * Code clean-up.  Renamed plugin classes to follow standard pattern
 *
 * Revision 1.7  2004/01/13 20:36:30  dicuccio
 * Use CBlastUtils for standard argument processing.  Make sure to pass the new
 * objects back to the framework with the appropriate action set (add to the
 * document specified)
 *
 * Revision 1.6  2003/12/22 19:25:56  dicuccio
 * Added check to see if no alignments were produced
 *
 * Revision 1.5  2003/11/26 21:08:07  ucko
 * Adjust for current CBlastOptions location and API.
 *
 * Revision 1.4  2003/11/06 20:12:12  dicuccio
 * Cleaned up handling of USING_SCOPE - removed from all headers
 *
 * Revision 1.3  2003/11/04 17:49:22  dicuccio
 * Changed calling parameters for plugins - pass CPluginMessage instead of paired
 * CPluginCommand/CPluginReply
 *
 * Revision 1.2  2003/11/03 17:41:19  dicuccio
 * Fixed to match changes in BLAST API
 *
 * Revision 1.1  2003/10/23 16:23:04  dicuccio
 * Moved code from algo/blast to algo/align
 *
 * Revision 1.3  2003/09/29 20:01:37  dicuccio
 * Fixed null dereference - must allocate annot.  Cleaned up access to parameters
 *
 * Revision 1.2  2003/09/29 19:28:01  dicuccio
 * Implemented variants of BLAST
 *
 * Revision 1.1  2003/09/25 17:41:10  dicuccio
 * Split BLAST plugin into three plugins, one each for BLASTn, BLASTp, and tBLASTn
 *
 * Revision 1.5  2003/09/04 18:36:23  dicuccio
 * Changed to use plugin_args namespace
 *
 * Revision 1.4  2003/09/04 14:05:24  dicuccio
 * Use IDocument instead of CDocument
 *
 * Revision 1.3  2003/08/21 12:03:08  dicuccio
 * Make use of new typedef in plugin_utils.hpp for argument values.
 *
 * Revision 1.2  2003/08/18 14:44:00  dicuccio
 * Partial fix for compilation issues
 *
 * Revision 1.1  2003/08/15 18:59:14  dicuccio
 * Initial revision
 *
 * ===========================================================================
 */