blast_base.cpp
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- /*
- * ===========================================================================
- * 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
- *
- * ===========================================================================
- */