prosite_search.cpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: prosite_search.cpp,v $
- * PRODUCTION Revision 1000.6 2004/06/01 20:55:39 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.23
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: prosite_search.cpp,v 1000.6 2004/06/01 20:55:39 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 searching against prosite patterns
- *
- */
- #include <ncbi_pch.hpp>
- #include "prosite_search.hpp"
- #include "prosite.hpp"
- #include <algo/sequence/find_pattern.hpp>
- #include <corelib/ncbiapp.hpp>
- #include <corelib/ncbireg.hpp>
- #include <gui/core/plugin_utils.hpp>
- #include <gui/utils/system_path.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/PluginRequest.hpp>
- #include <gui/plugin/PluginValueConstraint.hpp>
- #include <gui/utils/message_box.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_PrositeSearch::~CAlgoPlugin_PrositeSearch()
- {
- }
- // standard plugin announce bopilerplate
- void CAlgoPlugin_PrositeSearch::GetInfo(CPluginInfo& info)
- {
- info.Reset();
-
- // version info macro
- info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
- string(__DATE__) + " " + string(__TIME__),
- "CAlgoPlugin_PrositeSearch", "Search/Search against prosite",
- "Search a protein sequence against prosite patterns",
- "");
- // 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_aa));
- args.AddDefaultArgument("skip",
- "Skip patterns with SKIP_FLAG set",
- CPluginArg::eBoolean, "true");
- }
- void CAlgoPlugin_PrositeSearch::RunCommand(CPluginMessage& msg)
- {
- const CPluginCommand& args = msg.GetRequest().GetCommand();
- CPluginReply& reply = msg.SetReply();
- _TRACE("CAlgoPlugin_PrositeSearch::RunCommand()");
- bool skip = args["skip"].AsBoolean();
-
- // load patterns from file
- vector<CPrositeEntry> entries;
- try {
- x_LoadPrositeData(entries);
- }
- catch (const exception& e) {
- NcbiMessageBox(e.what());
- reply.SetStatus(eMessageStatus_failed);
- return;
- }
- if ( !m_Dialog.get() ) {
- m_Dialog.reset(new CMultiColDlg());
- m_Dialog->SetWindowSize(1000, 350);
- m_Dialog->SetTitle("Pattern Search Results");
- m_Dialog->SetColumn(0, "Sequence", FL_ALIGN_LEFT, 1.0f);
- m_Dialog->SetColumn(1, "Location", FL_ALIGN_LEFT, 1.0f);
- m_Dialog->SetColumn(2, "Position", FL_ALIGN_CENTER, 1.0f);
- m_Dialog->SetColumn(3, "Pattern ID", FL_ALIGN_LEFT, 3.0f);
- m_Dialog->SetColumn(4, "Pattern Description", FL_ALIGN_LEFT, 4.0f);
- m_Dialog->SetColumn(5, "Pattern", FL_ALIGN_LEFT, 3.0f);
- m_Dialog->SetColumn(6, "Matched Sequence", FL_ALIGN_LEFT, 2.0f);
- }
- m_Dialog->SetRows(0); // to clear any previous contents
-
- vector<TSeqPos> starts;
- vector<TSeqPos> ends;
- //
- // first, evaluate whole sequences
- //
- int row = 0;
- plugin_args::TLocList locs;
- GetArgValue(args["locs"], locs);
- unsigned int patterns_searched;
- 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());
- // a new feature table
- CRef<CSeq_annot> annot(new CSeq_annot());
- patterns_searched = 0;
- // iterate over patterns
- ITERATE (vector<CPrositeEntry>, entry, entries) {
- if (entry->GetSkipFlag() && skip) {
- continue; // skip this pattern entry
- }
- string pcre = CProsite::PSPatternToPCRE(entry->GetPattern());
- CFindPattern::Find(seq, pcre, starts, ends);
- patterns_searched++;
- for( unsigned int k = 0; k < starts.size(); k++) {
- 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) = entry->GetId();
- m_Dialog->SetCell(row, 4) = entry->GetDesc();
- m_Dialog->SetCell(row, 5) = entry->GetPattern();
- m_Dialog->SetCell(row, 6) =
- seq.substr(starts[k], ends[k] - starts[k] + 1);
- ++row;
- }
- //
- // add features to annot
- //
- for( unsigned int k = 0; k < starts.size(); k++) {
- // 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]);
- feat->SetLocation
- (*CSeqUtils::RemapChildToParent(loc, floc));
- // set feature data
- feat->SetData().SetRegion() = "Prosite match: "
- + entry->GetDesc() + "; "
- + entry->GetId();
-
- // save in annot
- annot->SetData().SetFtable().push_back(feat);
- }
- }
- // add description to annot
- annot->SetName("Prosite matches");
- // attach annot to doc
- //const_cast<IDocument&>(doc).AttachAnnot(*annot);
- reply.AddObject(doc, *annot);
- }
- catch (exception& e) {
- LOG_POST(Error << e.what());
- string str = CPluginUtils::GetLabel(loc, &doc.GetScope());
- LOG_POST(Error << "Error processing location " << str);
- }
- #ifndef _DEBUG
- catch (...) {
- string str = CPluginUtils::GetLabel(loc, &doc.GetScope());
- LOG_POST(Error << "Error processing location " << str);
- }
- #endif
- }
- // update all views
- //CDocManager::UpdateAllViews();
- //
- // prepare our dialog box
- //
- m_Dialog->SetLabel(string("A search against ")
- + NStr::IntToString(patterns_searched)
- + " patterns produced:");
- m_Dialog->Show();
- reply.SetStatus(eMessageStatus_success);
- reply.AddAction(CPluginReplyAction::e_Add_to_document);
- }
- void CAlgoPlugin_PrositeSearch::x_LoadPrositeData(vector<CPrositeEntry>& entries)
- {
- CNcbiApplication* app = CNcbiApplication::Instance();
- _ASSERT(app);
- CNcbiRegistry& registry = app->GetConfig();
- string fname;
- // By default the rebase "NAR format" file
- // is assumed to be <std>/etc/rebase.nar.
- // This can be overridden in gbench.ini, via the application registry
- // variable [PROSITE_SEARCH] PrositeData.
- fname = registry.GetString("PROSITE_SEARCH", "PrositeData", "");
- if ( !fname.empty() ) {
- fname += ", ";
- }
- fname += "<home>/etc/prosite.dat, <std>/etc/prosite.dat";
- fname = CSystemPath::ResolvePathExisting(fname);
- if ( fname.empty() ) {
- throw runtime_error("Couldn't open PROSITE file");
- }
-
- ifstream psfile(fname.c_str());
- CProsite::ReadEntries(psfile, entries);
- }
- END_NCBI_SCOPE
- /*
- * ===========================================================================
- * $Log: prosite_search.cpp,v $
- * Revision 1000.6 2004/06/01 20:55:39 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.23
- *
- * Revision 1.23 2004/05/21 22:27:47 gorelenk
- * Added PCH ncbi_pch.hpp
- *
- * Revision 1.22 2004/05/03 13:05:42 dicuccio
- * gui/utils --> gui/objutils where needed
- *
- * Revision 1.21 2004/03/05 17:35:37 dicuccio
- * Use sequence::GetId() instead of CSeq_id::GetStringDescr()
- *
- * Revision 1.20 2004/02/17 20:35:25 rsmith
- * moved core/settings.[ch]pp and core/system_path.[ch]pp to config and utils, respectively.
- *
- * Revision 1.19 2004/02/13 15:08:50 mjohnson
- * Removed local URL for plugin help.
- *
- * Revision 1.18 2004/01/27 18:38:08 dicuccio
- * Code clean-up. Use standard names for plugins. Removed unnecessary #includes
- *
- * Revision 1.17 2004/01/07 15:50:38 dicuccio
- * Adjusted for API change in CPluginUtils::GetLabel(). Standardized exception
- * reporting in algorithms.
- *
- * Revision 1.16 2003/12/15 20:16:08 jcherry
- * Changed CFindPattern::Find to take a string rather than a CSeqVector
- *
- * Revision 1.15 2003/11/24 15:45:28 dicuccio
- * Renamed CVersion to CPluginVersion
- *
- * Revision 1.14 2003/11/18 17:48:38 dicuccio
- * Added standard processing of return values
- *
- * Revision 1.13 2003/11/14 00:20:29 jcherry
- * Added url for help
- *
- * Revision 1.12 2003/11/06 20:12:12 dicuccio
- * Cleaned up handling of USING_SCOPE - removed from all headers
- *
- * Revision 1.11 2003/11/04 17:49:23 dicuccio
- * Changed calling parameters for plugins - pass CPluginMessage instead of paired
- * CPluginCommand/CPluginReply
- *
- * Revision 1.10 2003/10/27 17:46:49 dicuccio
- * Removed dead #includes
- *
- * Revision 1.9 2003/10/14 16:24:02 dicuccio
- * Added correct remapping of scanned locations to the parent location. Cleaned
- * up code to look for data file - added hierarchichal search through path in INI,
- * user's home directory, and finally system installed path.
- *
- * Revision 1.8 2003/10/07 13:47:00 dicuccio
- * Renamed CPluginURL* to CPluginValue*
- *
- * Revision 1.7 2003/09/25 17:21:35 jcherry
- * Added name to annot
- *
- * Revision 1.6 2003/09/04 14:05:24 dicuccio
- * Use IDocument instead of CDocument
- *
- * Revision 1.5 2003/09/03 14:46:53 rsmith
- * change namespace name from args to plugin_args to avoid clashes with variable names.
- *
- * Revision 1.4 2003/08/21 12:03:07 dicuccio
- * Make use of new typedef in plugin_utils.hpp for argument values.
- *
- * Revision 1.3 2003/08/15 18:48:06 jcherry
- * Brought dialog handling up to date.
- *
- * Revision 1.2 2003/08/11 18:03:25 jcherry
- * Fixed to use 0-based indexing for feature table (but retain
- * 1-based indexing for dialog box)
- *
- * Revision 1.1 2003/08/04 20:05:45 jcherry
- * Initial version
- *
- * ===========================================================================
- */