wbplg_aligner.cpp

来自「ncbi源码」· C++ 代码 · 共 559 行 · 第 1/2 页

        CRef<CSeq_align> align(new CSeq_align());
        CNWFormatter formatter (*aligner);
        formatter.AsSeqAlign(align);

        // we need to set the IDs correctly
        TIds::iterator seq_id_iter = seq_ids.begin();
        NON_CONST_ITERATE(CDense_seg::TIds, iter,
                          align->SetSegs().SetDenseg().SetIds()) {
            (*iter)->Assign(**seq_id_iter++);
        }

        // pack the alignment in a Seq-annot and label it appropriately
        CRef<CSeq_annot> annot(new CSeq_annot());
        annot->SetData().SetAlign().push_back(align);

        // prepare a title
        string str;
        ITERATE (vector<string>, iter, seq_labels) {
            if ( !str.empty() ) {
                str += " + ";
            }
            str += *iter;
        }

        str = "Global alignment of " + str;
        annot->AddTitle(str);

        CTime time;
        time.GetLocalTime();
        str = "This alignment was produced on ";
        str += time.AsString();
        str += " using the Needleman-Wunsch alignment algorithm";
        annot->AddComment(str);

        CRef<CAnnotdesc> desc(new CAnnotdesc());
        desc->SetCreate_date().SetStr(time.AsString());
        annot->SetDesc().Set().push_back(desc);

        //
        // 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, locs) {
            if ( !doc_ref ) {
                doc_ref.Reset(iter->first);
            } else if (iter->first != doc_ref) {
                doc_ref.Reset();
                break;
            }
        }

        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, locs) {
                new_scope->AddScope(iter->first->GetScope());
            }
            doc_ref.Reset(CDocManager::CreateDocument(*new_scope, *annot));
        } else {
            reply.AddAction(CPluginReplyAction::e_Add_to_document);
        }
        reply.AddObject(*doc_ref, *annot);
        reply.SetStatus(eMessageStatus_success);
    }
    catch (CException& e) {
        NcbiMessageBox("Global alignment failed:\n" + e.GetMsg());
    }
    catch(exception& e) {
        NcbiMessageBox(string("Global alignment failed:\n") + e.what());
    }
}


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: wbplg_aligner.cpp,v $
 * Revision 1000.4  2004/06/01 20:54:41  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.54
 *
 * Revision 1.54  2004/05/25 17:11:53  dicuccio
 * Deprecated old message box dialog in favor of standard progress dialog
 *
 * Revision 1.53  2004/05/21 22:27:46  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.52  2004/05/20 12:35:49  dicuccio
 * Removed dead code
 *
 * Revision 1.51  2004/05/17 15:11:44  kapustin
 * Initial revision
 *
 * Revision 1.50  2004/04/07 12:58:39  dicuccio
 * Removed dependence on gi for seq-id.  Changed default view to multiple
 * alignment view.  Cleaned up handling of view request / results processing
 *
 * Revision 1.49  2004/03/05 17:34:17  dicuccio
 * Use sequence::GetId() to retrieve GI-based ID
 *
 * Revision 1.48  2004/01/27 18:40:29  dicuccio
 * Code clean-up.  Renamed plugin classes to follow standard pattern
 *
 * Revision 1.47  2004/01/07 15:50:35  dicuccio
 * Adjusted for API change in CPluginUtils::GetLabel().  Standardized exception
 * reporting in algorithms.
 *
 * Revision 1.46  2003/12/22 19:26:29  dicuccio
 * Code reformatting.  Don't post a plugin message directly - use
 * CPluginUtils::CallPlugin()
 *
 * Revision 1.45  2003/12/09 15:46:16  dicuccio
 * Minor formatting change
 *
 * Revision 1.44  2003/11/24 15:45:24  dicuccio
 * Renamed CVersion to CPluginVersion
 *
 * Revision 1.43  2003/11/04 17:49:22  dicuccio
 * Changed calling parameters for plugins - pass CPluginMessage instead of paired
 * CPluginCommand/CPluginReply
 *
 * Revision 1.42  2003/10/27 17:47:04  dicuccio
 * Removed dead #includes
 *
 * Revision 1.41  2003/10/07 13:46:59  dicuccio
 * Renamed CPluginURL* to CPluginValue*
 *
 * Revision 1.40  2003/09/30 19:50:57  kapustin
 * Adjust for standard score matrix interface
 *
 * Revision 1.39  2003/09/04 14:05:23  dicuccio
 * Use IDocument instead of CDocument
 *
 * Revision 1.38  2003/09/03 14:46:52  rsmith
 * change namespace name from args to plugin_args to avoid clashes with variable names.
 *
 * Revision 1.37  2003/09/02 22:47:50  kapustin
 * Adjust for algo/align changes
 *
 * Revision 1.36  2003/09/02 17:08:06  rsmith
 * remove namespace name and variable name clash.
 *
 * Revision 1.35  2003/08/21 18:44:01  vasilche
 * Use CSeqVector::IsNucleotide() method instead of GetSequenceType().
 *
 * Revision 1.34  2003/08/21 12:03:07  dicuccio
 * Make use of new typedef in plugin_utils.hpp for argument values.
 *
 * Revision 1.33  2003/08/05 17:07:16  dicuccio
 * Changed calling semantics for the message queue - pass by reference, not
 * CConstRef<>
 *
 * Revision 1.32  2003/07/31 17:02:26  dicuccio
 * Changed plugin message queue class name to be application agnostic
 *
 * Revision 1.31  2003/07/23 19:14:09  dicuccio
 * Moved logic for validating plugin arguments into CPluginUtils.
 *
 * Revision 1.30  2003/07/22 15:32:15  dicuccio
 * Changed to make use of new API in plugin_utils.hpp - GetArgValue()
 *
 * Revision 1.29  2003/07/14 11:10:18  shomrat
 * Plugin messageing system related changes
 *
 * Revision 1.28  2003/06/26 15:33:40  dicuccio
 * Moved GetURLValue() from PluginURL.hpp to plugin_utils.hpp.  Fixed
 * compilation errors relating to missing #includes
 *
 * Revision 1.27  2003/06/25 17:02:56  dicuccio
 * Split CPluginHandle into a handle (pointer-to-implementation) and
 * implementation file.  Lots of #include file clean-ups.
 *
 * Revision 1.26  2003/06/20 14:52:35  dicuccio
 * Revised plugin registration - moved GetInfo() into the plugin handler
 *
 * Revision 1.25  2003/06/17 16:41:43  dicuccio
 * Fix #includes after algo/ rearrangement
 *
 * Revision 1.24  2003/06/09 19:25:58  dicuccio
 * Added <stdio.h> for sprintf()
*
* Revision 1.23  2003/06/02 16:06:20  dicuccio
* Rearranged src/objects/ subtree.  This includes the following shifts:
*     - src/objects/asn2asn --> arc/app/asn2asn
*     - src/objects/testmedline --> src/objects/ncbimime/test
*     - src/objects/objmgr --> src/objmgr
*     - src/objects/util --> src/objmgr/util
*     - src/objects/alnmgr --> src/objtools/alnmgr
*     - src/objects/flat --> src/objtools/flat
*     - src/objects/validator --> src/objtools/validator
*     - src/objects/cddalignview --> src/objtools/cddalignview
* In addition, libseq now includes six of the objects/seq... libs, and libmmdb
* replaces the three libmmdb? libs.
*
* Revision 1.22  2003/05/30 20:23:43  kapustin
* Fix sequence index typo
*
* Revision 1.21  2003/05/30 20:05:43  kapustin
* Support arbitrarily sized sequences
*
* Revision 1.20  2003/05/19 13:38:32  dicuccio
* Moved gui/core/plugin/ --> gui/plugin/.  Merged core libraries
* into libgui_core
*
* Revision 1.19  2003/05/12 16:08:40  dicuccio
* Updated to use new plugin action args
*
* Revision 1.18  2003/05/08 18:27:56  kapustin
* Allow specification of plugin's arguments
*
* Revision 1.17  2003/04/30 14:09:42  dicuccio
* Updated Needleman-Wunsch plugin - produce a Seq-annot as a document;
* launch a default graphical view (cross alignment viewer)
    *
    * Revision 1.16  2003/04/24 16:37:30  dicuccio
    * Updated to reflect changes in plugin API
    *
    * Revision 1.15  2003/04/22 16:29:00  kapustin
    * Fix memory limit typo
    *
    * Revision 1.14  2003/04/22 16:18:36  kapustin
    * Support aminoacid sequences. Set memory limit.
    *
    * Revision 1.13  2003/04/03 01:08:24  ucko
    * Adjust for new FormatAsText interface.
    *
    * Revision 1.12  2003/03/12 21:12:47  kapustin
    * Use text buffer provided by the aligner to store text messages
    *
    * Revision 1.11  2003/03/11 15:23:29  kuznets
    * iterate -> ITERATE
    *
    * Revision 1.10  2003/03/05 21:23:11  kapustin
    * Reflect new CNWAligner::FormatAsText() call
    *
    * Revision 1.9  2003/02/26 14:31:46  dicuccio
    * General clean-up.  Fixed passing of arguments - alignment should work now.
    *
    * Revision 1.8  2003/02/25 14:44:34  dicuccio
    * Changed accessors to match API changes in plugin arguments
    *
    * Revision 1.7  2003/02/24 13:03:14  dicuccio
    * Renamed classes in plugin spec:
    *     CArgSeg --> CPluginArgSet
    *     CArgument --> CPluginArg
    *     CPluginArgs --> CPluginCommand
    *     CPluginCommands --> CPluginCommandSet
    *
    * Revision 1.6  2003/02/21 17:13:54  dicuccio
    * Changed enums in CDlgMessageBox - added leading 'e' to avoid
    * impossible-to-remove conflict with Windows code.
    *
    * Revision 1.5  2003/02/20 19:49:53  dicuccio
    * Created new plugin architecture, based on ASN.1 spec. Moved GBENCH frameowrk
    * over to use new plugin architecture.
    *
    * Revision 1.4  2003/02/05 17:23:21  ucko
    * When going from CNcbiOstrstream to char* via CNcbiOstrstreamToString,
    * explicitly use an intermediate string variable to avoid confusing some
    * compilers (GCC 2.9x at least).
    *
    * Revision 1.3  2003/02/04 22:58:33  kapustin
    * Split plugin activation into x_Verify() and x_Run(). Add progress callback
    *
    * Revision 1.2  2003/01/29 19:39:54  kapustin
    * Increase output line width
    *
    * Revision 1.1  2003/01/29 19:10:37  kapustin
    * Initial revision
    *
    * ===========================================================================
    */