featid_table.cpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: featid_table.cpp,v $
- * PRODUCTION Revision 1000.1 2004/06/01 21:00:37 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.3
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: featid_table.cpp,v 1000.1 2004/06/01 21:00:37 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 "featid_table.hpp"
- #include <objects/general/Dbtag.hpp>
- #include <objects/general/Object_id.hpp>
- #include <objects/seqloc/Seq_interval.hpp>
- #include <objmgr/util/sequence.hpp>
- #include <set>
- #include <serial/iterator.hpp>
- BEGIN_NCBI_SCOPE
- USING_SCOPE(objects);
- CFeatIdTable::CFeatIdTable(int x, int y, int w, int h, const char* label)
- : CTablePanel< CConstRef<CSeq_loc> >(x, y, w, h, label)
- {
- SetColumn(0, "Source", eString, FL_ALIGN_LEFT, 0.5f);
- SetColumn(1, "Database", eString, FL_ALIGN_LEFT, 0.5f);
- SetColumn(2, "Identifier", eString, FL_ALIGN_LEFT, 1.0f);
- }
- void CFeatIdTable::Update(const CSeq_feat& feat)
- {
- size_t row = 0;
- // IDs from main location
- {{
- SetCell(row, 0) = "Sequence";
- // use the whole spanned location, not the original location
- const CSeq_id& id = sequence::GetId(feat.GetLocation());
- CRef<CSeq_loc> loc(new CSeq_loc());
- loc->SetInt().SetFrom(feat.GetLocation().GetTotalRange().GetFrom());
- loc->SetInt().SetTo(feat.GetLocation().GetTotalRange().GetTo());
- loc->SetInt().SetStrand(sequence::GetStrand(feat.GetLocation()));
- loc->SetId(id);
- SetData(row, loc);
- SetCell(row, 1, x_GetSource(id));
- SetCell(row, 2, id.AsFastaString());
- ++row;
- }}
- // IDs from the product location, if it exists
- if (feat.IsSetProduct()) {
- SetCell(row, 0, "Product");
- SetData(row, CConstRef<CSeq_loc>(&feat.GetProduct()));
- const CSeq_id& id = sequence::GetId(feat.GetProduct());
- SetCell(row, 1, x_GetSource(id));
- SetCell(row, 2, id.AsFastaString());
- ++row;
- }
- // IDs from DB xrefs
- if (feat.IsSetDbxref()) {
- SetCell(row, 0, "External DB");
- ITERATE (CSeq_feat::TDbxref, iter, feat.GetDbxref()) {
- const CDbtag& tag = **iter;
- CRef<CSeq_loc> loc(new CSeq_loc());
- loc->SetWhole(*x_GetSeqId(tag));
- SetData(row, loc);
- SetCell(row, 1, tag.GetDb());
- if (tag.GetTag().IsStr()) {
- SetCell(row, 2, tag.GetTag().GetStr());
- } else {
- SetCell(row, 2, NStr::UIntToString(tag.GetTag().GetId()));
- }
- ++row;
- }
- }
- }
- // get a string describing the source of a given seq-id
- string CFeatIdTable::x_GetSource(const CSeq_id& id) const
- {
- switch (id.Which()) {
- case CSeq_id::e_Local:
- return "Local";
- case CSeq_id::e_Gibbsq:
- case CSeq_id::e_Gibbmt:
- return "Geninfo Backbone";
- case CSeq_id::e_Giim:
- return "Geninfo Import";
- case CSeq_id::e_Genbank:
- return "Genbank";
- case CSeq_id::e_Embl:
- return "EMBL";
- case CSeq_id::e_Pir:
- return "PIR";
- case CSeq_id::e_Swissprot:
- return "Swiss-PROT";
- case CSeq_id::e_Patent:
- return "Patent";
- case CSeq_id::e_Other:
- return "Other";
- case CSeq_id::e_General:
- return "General";
- case CSeq_id::e_Gi:
- return "Genbank ID";
- case CSeq_id::e_Ddbj:
- return "DDBJ";
- case CSeq_id::e_Prf:
- return "Prf Sequence";
- case CSeq_id::e_Pdb:
- return "PDB";
- case CSeq_id::e_Tpg:
- return "Third-Party";
- case CSeq_id::e_Tpe:
- return "Third-Party/EMBL";
- case CSeq_id::e_Tpd:
- return "Third-Party/DDBJ";
- default:
- return "Unknown";
- break;
- }
- }
- // get a seq-id for a given Dbtag
- CSeq_id* CFeatIdTable::x_GetSeqId(const CDbtag& dbtag) const
- {
- static map<string, string> s_IdDictionary;
- if (s_IdDictionary.size() == 0) {
- s_IdDictionary["ENSEMBL"] = "lcl|";
- s_IdDictionary["GenBank"] = "gb|";
- s_IdDictionary["RefSeq" ] = "ref|";
- s_IdDictionary["EMBL" ] = "gb|";
- s_IdDictionary["DDBJ" ] = "gb|";
- }
- string str(dbtag.GetDb() + "|");
- map<string, string>::const_iterator iter =
- s_IdDictionary.find(dbtag.GetDb());
- if (iter != s_IdDictionary.end()) {
- str = iter->second;
- }
- if (dbtag.GetTag().IsStr()) {
- str += dbtag.GetTag().GetStr();
- } else {
- str += NStr::UIntToString(dbtag.GetTag().GetId());
- }
- CRef<CSeq_id> id(new CSeq_id(str));
- if (id->Which() == CSeq_id::e_not_set) {
- id.Reset(new CSeq_id("lcl|" + str));
- }
- return id.Release();
- }
- END_NCBI_SCOPE
- /*
- * ===========================================================================
- * $Log: featid_table.cpp,v $
- * Revision 1000.1 2004/06/01 21:00:37 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.3
- *
- * Revision 1.3 2004/05/21 22:27:49 gorelenk
- * Added PCH ncbi_pch.hpp
- *
- * Revision 1.2 2004/01/20 18:17:53 dicuccio
- * Changed to match new API in CTablePanel
- *
- * Revision 1.1 2004/01/13 20:38:46 dicuccio
- * Added new view: feature IDs
- *
- * ===========================================================================
- */
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