run_cn3d.cpp

来自「ncbi源码」· C++ 代码 · 共 289 行

/*
 * ===========================================================================
 * PRODUCTION $Log: run_cn3d.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 20:55:55  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.7
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: run_cn3d.cpp,v 1000.1 2004/06/01 20:55:55 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:  Josh Cherry
 *
 * File Description:  gbench plugin for invoking Cn3D
 *
 */


#include <ncbi_pch.hpp>
#include "run_cn3d.hpp"

#include <gui/core/idocument.hpp>
#include <gui/core/plugin_utils.hpp>
#include <gui/plugin/PluginCommandSet.hpp>
#include <gui/plugin/PluginValue.hpp>
#include <gui/plugin/PluginInfo.hpp>
#include <gui/plugin/PluginReply.hpp>
#include <gui/plugin/PluginRequest.hpp>
#include <gui/plugin/PluginValueConstraint.hpp>
#include <gui/core/version.hpp>
#include <gui/core/doc_manager.hpp>
#include <gui/objutils/utils.hpp>
#include <gui/utils/message_box.hpp>
#include <FL/Fl_File_Chooser.H>

#include <gui/utils/file_deletion.hpp>
#include <corelib/ncbifile.hpp>
#include <corelib/ncbiexec.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbireg.hpp>

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

#include <objects/seq/Bioseq.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/ncbimime/Ncbi_mime_asn1.hpp>
#include <objects/ncbimime/Biostruc_seqs_aligns_cdd.hpp>
#include <objects/ncbimime/Bundle_seqs_aligns.hpp>
#include <objects/seqalign/Dense_seg.hpp>


BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


// standard info boilerplate
void CAlgoPlugin_RunCn3d::GetInfo(CPluginInfo& info)
{
    info.Reset();

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CAlgoPlugin_RunCn3d",
                 "Alignments/Launch Cn3D",
                 "Invoke the Cn3D program",
                 "");

    // command info
    CPluginCommandSet& cmds = info.SetCommands();
    CPluginCommand&    args = cmds.AddAlgoCommand(eAlgoCommand_run);

    args.AddArgument("aligns", "Input alignment(s)",
                     CSeq_align::GetTypeInfo(),
                     CPluginArg::TData::e_Array);
}


struct SIdLess
{
public:
    bool operator() (CRef<CSeq_id> lhs, CRef<CSeq_id> rhs) {
        return *lhs < *rhs;
    }
};


// Given a multiple alignment (Dense-seg), express as multiple pairwise
// alignments, and append these to list.
// The first sequence in the input alignment is the first sequence
// in each of the aln.GetDim() - 1 pairwise alignments. 
static void s_AsPairwise(const CSeq_align& aln,
                         CSeq_annot::C_Data::TAlign& pairs)
{
    const CDense_seg& ds = aln.GetSegs().GetDenseg();
    vector<CRef<CDense_seg> > dss(aln.GetSegs().GetDenseg().GetDim() - 1);
    CDense_seg::TIds::const_iterator id = ds.GetIds().begin(); ++id;
    CDense_seg::TStrands::const_iterator strand;
    if (ds.IsSetStrands()) {
        strand = ds.GetStrands().begin();
        ++strand;
    }
    NON_CONST_ITERATE (vector<CRef<CDense_seg> >, iter, dss) {
        *iter = new CDense_seg;
        (*iter)->SetNumseg(ds.GetNumseg());

        (*iter)->SetIds().push_back(ds.GetIds().front());
        (*iter)->SetIds().push_back(*id);
        ++id;

        (*iter)->SetLens() = ds.GetLens();

        if (ds.IsSetStrands()) {
            (*iter)->SetStrands().push_back(ds.GetStrands().front());
            (*iter)->SetStrands().push_back(*strand);
            ++strand;
        }
    }

    unsigned int i = 0;
    ITERATE (CDense_seg::TStarts, iter, ds.GetStarts()) {
        if (i % ds.GetDim()) {
            dss[i % ds.GetDim() - 1]->SetStarts().push_back(*iter);
        } else {
            // start for master sequence; goes in all pairwise
            for (unsigned int p = 0;  p < dss.size();  ++p) {
                dss[p]->SetStarts().push_back(*iter);
            }
        }
        ++i;
    }

    // have Dense-segs; make Seq-aligns and append
    for (unsigned int p = 0;  p < dss.size();  ++p) {
        CRef<CSeq_align> pairwise(new CSeq_align);
        pairwise->SetType(CSeq_align::eType_partial);
        pairwise->SetDim(2);
        pairwise->SetSegs().SetDenseg(*dss[p]);
        pairs.push_back(pairwise);
    }
}


void CAlgoPlugin_RunCn3d::RunCommand(CPluginMessage& msg)
{

    const CPluginCommand& args = msg.GetRequest().GetCommand();
    CPluginReply& reply = msg.SetReply();
    _TRACE("CAlgoPlugin_RunCn3d::Run()");

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


    // build a Ncbi-mime-asn1 object around alignments

    CRef<CSeq_annot> annot(new CSeq_annot);
    typedef map<CRef<CSeq_id>, CScope *, SIdLess> TIdScopeMap;
    TIdScopeMap ids;

    ITERATE (plugin_args::TAlignList, iter, aligns) {
        s_AsPairwise(*iter->second, annot->SetData().SetAlign());
        ITERATE (CDense_seg::TIds, id,
                 iter->second->GetSegs().GetDenseg().GetIds()) {
            ids.insert(make_pair(*id, &iter->first->GetScope()));
        }
    }
    
    CRef<CNcbi_mime_asn1> mime(new CNcbi_mime_asn1);
    mime->SetGeneral().SetSeq_align_data().SetBundle().SetSeqaligns()
        .push_back(annot);

    ITERATE (TIdScopeMap, iter, ids) {
        CRef<CBioseq> bs(new CBioseq);
        CRef<CSeq_entry> entry(new CSeq_entry);
        bs->Assign(*(iter->second)->GetBioseqHandle(*(iter->first))
                      .GetCompleteBioseq());
        entry->SetSeq(*bs);
        mime->SetGeneral().SetSeq_align_data().SetBundle().SetSequences()
            .push_back(entry);
    }


    // Write it to a temp file and launch the app

    string fname = CFile::GetTmpName();
    {{
        auto_ptr<CObjectOStream>
            ostr(CObjectOStream::Open(eSerial_AsnText, fname));
        *ostr << *mime;
    }}
    CDeleteAtExit::Add(fname);

    // Try to run Cn3D.  The path to the executable can
    // come from the registry.  Otherwise "Cn3D" is tried.
    CNcbiApplication* app = CNcbiApplication::Instance();
    _ASSERT(app);
    CNcbiRegistry& registry = app->GetConfig();
    string path = registry.GetString("external_apps", "cn3d", "Cn3D");
    bool new_path = 0;  // has a new path been set?
    int phandle;
    int status;
    while (1) {
        phandle = CExec::SpawnLP(CExec::eDetach, path.c_str(),
                                 fname.c_str(), 0);
        // this is a dicey way of finding out whether
        // the spawn was successful
        status = CExec::Wait(phandle, 1000);
        if (status == -1) {
            break;
        }

        const char *text = 
            fl_file_chooser("Please locate the Cn3D application", "*", "");
        if ( !text  ||  !*text ) {
            break;
        }
        path = text;
        new_path = true;
    }

    if (status == -1) {
        reply.SetStatus(eMessageStatus_success);
        if (new_path) {
            registry.Set("external_apps", "cn3d", path,
                         CNcbiRegistry::ePersistent);
        }
    }
}


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: run_cn3d.cpp,v $
 * Revision 1000.1  2004/06/01 20:55:55  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.7
 *
 * Revision 1.7  2004/05/21 22:27:47  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.6  2004/05/20 12:37:58  dicuccio
 * Added missing include for CDense_seg
 *
 * Revision 1.5  2004/05/15 03:17:04  ucko
 * Add missing #includes (formerly indirect?)
 *
 * Revision 1.4  2004/05/03 13:05:42  dicuccio
 * gui/utils --> gui/objutils where needed
 *
 * Revision 1.3  2004/04/16 17:23:06  ucko
 * GetCompleteBioseq returns a CConstRef rather than a C++ reference.
 *
 * Revision 1.2  2004/04/16 14:43:37  dicuccio
 * Use GetCompleteBioseq() instead of GetBioseq()
 *
 * Revision 1.1  2004/03/05 16:44:22  jcherry
 * Initial version
 *
 * ===========================================================================
 */