nmer_repeats.cpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: nmer_repeats.cpp,v $
- * PRODUCTION Revision 1000.1 2004/06/01 20:55:10 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: nmer_repeats.cpp,v 1000.1 2004/06/01 20:55:10 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 finding nmer repeats
- *
- */
- #include <ncbi_pch.hpp>
- #include "nmer_repeats.hpp"
- #include <algo/sequence/find_pattern.hpp>
- #include <gui/core/plugin_utils.hpp>
- #include <gui/core/version.hpp>
- #include <gui/dialogs/col/multi_col_dlg.hpp>
- #include <gui/plugin/PluginCommandSet.hpp>
- #include <gui/plugin/PluginInfo.hpp>
- #include <gui/plugin/PluginReply.hpp>
- #include <gui/plugin/PluginRequest.hpp>
- #include <gui/plugin/PluginValueConstraint.hpp>
- #include <gui/objutils/utils.hpp>
- #include <objects/seqloc/Seq_interval.hpp>
- #include <objmgr/seq_vector.hpp>
- #include <objmgr/util/sequence.hpp>
- BEGIN_NCBI_SCOPE
- USING_SCOPE(objects);
- CAlgoPlugin_NmerRepeats::~CAlgoPlugin_NmerRepeats()
- {
- }
- // standard plugin announce bopilerplate
- void CAlgoPlugin_NmerRepeats::GetInfo(CPluginInfo& info)
- {
- info.Reset();
-
- // version info macro
- info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
- string(__DATE__) + " " + string(__TIME__),
- "CAlgoPlugin_NmerRepeats", "Search/Find n-mer repeats",
- "Find di-, tri-, and tetra-nucleotide repeats",
- "");
- // command info
- CPluginCommandSet& cmds = info.SetCommands();
- CPluginCommand& args = cmds.AddAlgoCommand(eAlgoCommand_run);
- args.AddArgument("locs", "Locations to evaluate",
- CSeq_loc::GetTypeInfo(),
- CPluginArg::TData::e_Array);
- args.SetConstraint("locs",
- (*CPluginValueConstraint::CreateSeqMol(),
- CSeq_inst::eMol_na,
- CSeq_inst::eMol_dna,
- CSeq_inst::eMol_rna));
- args.AddDefaultArgument("dinuc_min",
- "Minimum number of dinuclotide units",
- CPluginArg::eInteger, "5");
- args.AddDefaultArgument("trinuc_min",
- "Minimum number of trinuclotide units",
- CPluginArg::eInteger, "5");
- args.AddDefaultArgument("tetranuc_min",
- "Minimum number of tetranuclotide units",
- CPluginArg::eInteger, "5");
- }
- void CAlgoPlugin_NmerRepeats::RunCommand(CPluginMessage& msg)
- {
- const CPluginCommand& args = msg.GetRequest().GetCommand();
- CPluginReply& reply = msg.SetReply();
- _TRACE("CAlgoPlugin_NmerRepeats::Run()");
- vector<int> minima(5);
- minima[2] = args["dinuc_min"].AsInteger();
- minima[3] = args["trinuc_min"].AsInteger();
- minima[4] = args["tetranuc_min"].AsInteger();
- if ( !m_Dialog.get() ) {
- m_Dialog.reset(new CMultiColDlg());
- m_Dialog->SetWindowSize(600, 350);
- m_Dialog->SetTitle("n-mer Nucleotide Repeats");
- m_Dialog->SetLabel("Search results:");
- m_Dialog->SetColumn(0, "Sequence");
- m_Dialog->SetColumn(1, "Location");
- m_Dialog->SetColumn(2, "Position", FL_ALIGN_CENTER, 2.0);
- m_Dialog->SetColumn(3, "Repeat", FL_ALIGN_LEFT);
- }
- // clear any previous contents
- m_Dialog->SetRows(0);
- vector<TSeqPos> starts;
- vector<TSeqPos> ends;
- int row = 0;
- plugin_args::TLocList locs;
- GetArgValue(args["locs"], locs);
- ITERATE (plugin_args::TLocList, iter, locs) {
- const CSeq_loc& loc = *iter->second;
- const IDocument& doc = *iter->first;
- // find the best ID for this bioseq
- try {
- CBioseq_Handle handle = doc.GetScope().GetBioseqHandle(loc);
- CSeqVector vec =
- handle.GetSequenceView(loc,
- CBioseq_Handle::eViewConstructed,
- CBioseq_Handle::eCoding_Iupac);
- string seq;
- vec.GetSeqData( (TSeqPos) 0, vec.size(), seq );
- string& id_str = m_Dialog->SetCell(row, 0);
- string& loc_str = m_Dialog->SetCell(row, 1);
- const CSeq_id& best_id =
- sequence::GetId(handle, sequence::eGetId_Best);
- id_str.erase();
- best_id.GetLabel(&id_str);
- loc_str = CPluginUtils::GetLabel(loc, &doc.GetScope());
- CRef<CSeq_annot> annot(new CSeq_annot());
- string rep_unit;
- int rep_num;
- string rep_summary;
- for (unsigned int n = 2; n <= 4; ++n) {
- starts.clear();
- ends.clear();
- CFindPattern::FindNucNmerRepeats(seq, n, minima[n],
- starts, ends);
- // preallocate rows in dialog for speed
- m_Dialog->SetRows(row + starts.size());
- for(unsigned int k = 0; k < starts.size(); k++) {
- rep_unit = seq.substr(starts[k], n);
-
- if (rep_unit.find_first_not_of(rep_unit.substr(0, 1), 1)
- == string::npos) {
- // skip it if it's a monomer repeat
- continue;
- }
-
- if (n == 4) {
- // check whether it's a dimer repeat too
- if (rep_unit[2] == rep_unit[0] &&
- rep_unit[3] == rep_unit[1]) {
- // if so, skip it
- continue;
- }
- }
- rep_num = (ends[k] - starts[k] + 1) / n;
- rep_summary = "(" + rep_unit + ")" +
- NStr::IntToString(rep_num);
- string& pos_str = m_Dialog->SetCell(row, 2);
- // 1-based indexing for dialog
- pos_str = NStr::IntToString(starts[k] + 1) + " - "
- + NStr::IntToString(ends[k] + 1);
- m_Dialog->SetCell(row, 3) = rep_summary;
-
- ++row;
- // create feature
- CRef<CSeq_feat> feat(new CSeq_feat());
- // set correct location
- {{
- CSeq_loc& floc = feat->SetLocation();
- floc.SetInt().SetId().Assign(sequence::GetId(loc));
- floc.SetInt().SetFrom(starts[k]);
- floc.SetInt().SetTo(ends[k]);
- floc.SetInt().SetStrand(eNa_strand_plus);
- CRef<CSeq_loc> new_loc =
- CSeqUtils::RemapChildToParent(loc, floc);
- feat->SetLocation(*new_loc);
- }}
- // set feature data
- feat->SetData().SetRegion() = "Repeat: " + rep_summary;
-
- // save in annot
- annot->SetData().SetFtable().push_back(feat);
- }
- }
- // add description to annot
- annot->AddName("n-mer Repeats");
- reply.AddObject(doc, *annot);
- }
- catch (CException& e) {
- string str = CPluginUtils::GetLabel(loc, &doc.GetScope());
- LOG_POST(Error << "Error processing location " << str
- << ": " << e.what());
- }
- #ifndef _DEBUG
- catch (...) {
- string str = CPluginUtils::GetLabel(loc, &doc.GetScope());
- LOG_POST(Error << "Error processing location " << str);
- }
- #endif
- }
- //
- // prepare our dialog box
- //
- m_Dialog->SetRows(row);
- m_Dialog->Show();
- reply.AddAction(CPluginReplyAction::e_Add_to_document);
- reply.SetStatus(eMessageStatus_success);
- }
- END_NCBI_SCOPE
- /*
- * ===========================================================================
- * $Log: nmer_repeats.cpp,v $
- * Revision 1000.1 2004/06/01 20:55:10 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
- *
- * Revision 1.6 2004/05/21 22:27:46 gorelenk
- * Added PCH ncbi_pch.hpp
- *
- * Revision 1.5 2004/05/03 13:05:42 dicuccio
- * gui/utils --> gui/objutils where needed
- *
- * Revision 1.4 2004/03/05 17:35:37 dicuccio
- * Use sequence::GetId() instead of CSeq_id::GetStringDescr()
- *
- * Revision 1.3 2004/01/27 18:37:47 dicuccio
- * Code clean-up. Use standard names for plugins. Removed unnecessary #includes
- *
- * Revision 1.2 2004/01/07 15:50:37 dicuccio
- * Adjusted for API change in CPluginUtils::GetLabel(). Standardized exception
- * reporting in algorithms.
- *
- * Revision 1.1 2003/12/17 17:35:09 jcherry
- * Initial version
- *
- * ===========================================================================
- */