align_merge.cpp

来自「ncbi源码」· C++ 代码 · 共 213 行

/*
 * ===========================================================================
 * PRODUCTION $Log: align_merge.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 20:54:07  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.2
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: align_merge.cpp,v 1000.1 2004/06/01 20:54:07 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:  Yuri Kapustin
 *
 * File Description:
 *    CAlgoPlugin_AlignMerge -- wraps global alignment algorithms
 */


#include <ncbi_pch.hpp>
#include "align_merge.hpp"
#include <gui/core/version.hpp>
#include <gui/core/plugin_utils.hpp>
#include <gui/utils/message_box.hpp>
#include <gui/plugin/PluginInfo.hpp>
#include <gui/plugin/PluginRequest.hpp>
#include <gui/plugin/PluginReply.hpp>
#include <gui/plugin/PluginCommand.hpp>
#include <gui/plugin/PluginCommandSet.hpp>
#include <gui/plugin/PluginArgSet.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objtools/alnmgr/alnmix.hpp>

BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


// GetInfo()
// static interface to retrieve plugin registration information
void CAlgoPlugin_AlignMerge::GetInfo(CPluginInfo& info)
{
    info.Reset();

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CAlgoPlugin_AlignMerge",
                 "Alignments/Merge Alignments",
                 "Create a pseudomultiple alignment from a set of alignments",
                 "");

    // command info
    CPluginCommandSet& cmds = info.SetCommands();
    CPluginCommand&    cmd = cmds.AddAlgoCommand(eAlgoCommand_run);
    cmd.AddArgument("aligns", "Alignments to merge",
                     CSeq_align::GetTypeInfo(),
                     CPluginArg::TData::e_Array);

    cmd.AddDefaultFlag("gen2est",
                        "Genomic <-> EST Alignment", true);
    cmd.AddDefaultFlag("no_objmgr",
                        "Don't fetch sequences",     false);
    cmd.AddDefaultFlag("calc_score",
                        "Recalculate scores",        true);
    cmd.AddDefaultFlag("force_trans",
                        "Force translation",         false);
    cmd.AddDefaultFlag("truncate",
                        "Truncate overlapping segments", false);
    cmd.AddDefaultFlag("neg_strand",
                        "Assume all on negative strand", false);
    cmd.AddDefaultFlag("gap_join",
                        "Join gaps where possible",  true);
    cmd.AddDefaultFlag("min_gap",
                        "Compress gaps where possible", true);
    cmd.AddDefaultFlag("score_sort",
                        "Sort by scores",            true);
    cmd.AddDefaultFlag("query_merge",
                        "Merge query sequence only", false);
    cmd.AddDefaultFlag("fill_unaligned",
                        "Fill unaligned regions",    false);
}


void CAlgoPlugin_AlignMerge::RunCommand(CPluginMessage& msg)
{
    const CPluginCommand& cmd = msg.GetRequest().GetCommand();
    CPluginReply& reply = msg.SetReply();
    reply.SetStatus(eMessageStatus_failed);

    // retrieve our alignments
    plugin_args::TAlignList aligns;
    GetArgValue(cmd["aligns"], aligns);

    CAlnMix::TAddFlags   add_flags = 0;
    CAlnMix::TMergeFlags merge_flags = 0;
    if (cmd["gen2est"].AsBoolean()) {
        merge_flags |= CAlnMix::fGen2EST;
    }
    if (cmd["no_objmgr"].AsBoolean()) {
        add_flags |= CAlnMix::fDontUseObjMgr;
    }
    if (cmd["calc_score"].AsBoolean()) {
        add_flags |= CAlnMix::fCalcScore;
    }
    if (cmd["force_trans"].AsBoolean()) {
        add_flags |= CAlnMix::fForceTranslation;
    }
    if (cmd["truncate"].AsBoolean()) {
        merge_flags |= CAlnMix::fTruncateOverlaps;
    }
    if (cmd["neg_strand"].AsBoolean()) {
        merge_flags |= CAlnMix::fNegativeStrand;
    }
    if (cmd["gap_join"].AsBoolean()) {
        merge_flags |= CAlnMix::fGapJoin;
    }
    if (cmd["min_gap"].AsBoolean()) {
        merge_flags |= CAlnMix::fMinGap;
    }
    if (cmd["score_sort"].AsBoolean()) {
        merge_flags |= CAlnMix::fSortSeqsByScore;
    }
    if (cmd["query_merge"].AsBoolean()) {
        merge_flags |= CAlnMix::fQuerySeqMergeOnly;
    }
    if (cmd["fill_unaligned"].AsBoolean()) {
        merge_flags |= CAlnMix::fFillUnalignedRegions;
    }

    set< CConstRef<IDocument> > docs;
    ITERATE (plugin_args::TAlignList, iter, aligns) {
        docs.insert(iter->first);
    }

    if (docs.size() != 1) {
        NcbiMessageBox("Failed to merge alignments:\n"
                       "All alignments must be in the same document");
        return;
    }

    try {
        CConstRef<IDocument> doc = *docs.begin();
        CAlnMix mix(doc->GetScope());
        ITERATE (plugin_args::TAlignList, iter, aligns) {
            mix.Add(*iter->second, add_flags);
        }

        mix.Merge(merge_flags);

        CRef<CSeq_annot> annot(new CSeq_annot());
        annot->SetName("Merged Alignment");
        annot->SetData().SetAlign().push_back
            (CRef<CSeq_align>(const_cast<CSeq_align*>(&mix.GetSeqAlign())));

        reply.AddObject(*doc, *annot);
        reply.AddAction(CPluginReplyAction::e_Add_to_document);
        reply.SetStatus(eMessageStatus_success);
    }
    catch (CException& e) {
        NcbiMessageBox("Failed to merge alignments:\n" +
                       e.GetMsg());
        return;
    }
#ifndef _DEBUG
    catch (...) {
        NcbiMessageBox("Failed to merge alignments:\n"
                       "Unknown error.");
        return;
    }
#endif
}


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: align_merge.cpp,v $
 * Revision 1000.1  2004/06/01 20:54:07  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.2
 *
 * Revision 1.2  2004/05/21 22:27:46  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.1  2004/01/27 18:39:05  dicuccio
 * Initial revision
 *
 * ===========================================================================
 */