lds_reader.cpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: lds_reader.cpp,v $
- * PRODUCTION Revision 1000.1 2004/06/01 19:45:52 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: lds_reader.cpp,v 1000.1 2004/06/01 19:45:52 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.
- *
- * ===========================================================================
- *
- * Author: Anatoliy Kuznetsov
- *
- * File Description: LDS reader implementation.
- *
- */
- #include <ncbi_pch.hpp>
- #include <corelib/ncbifile.hpp>
- #include <util/format_guess.hpp>
- #include <bdb/bdb_cursor.hpp>
- #include <serial/objistr.hpp>
- #include <objects/seq/Bioseq.hpp>
- #include <objects/seqalign/Seq_align.hpp>
- #include <objmgr/util/obj_sniff.hpp>
- #include <objtools/readers/fasta.hpp>
- #include <objtools/lds/lds_reader.hpp>
- #include <objtools/lds/lds_db.hpp>
- #include <objtools/lds/lds_expt.hpp>
- #include <objtools/lds/lds_query.hpp>
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(objects)
- CRef<CSeq_entry> LDS_LoadTSE(SLDS_TablesCollection& db,
- const map<string, int>& type_map,
- int object_id)
- {
- CLDS_Query query(db);
- CLDS_Query::SObjectDescr obj_descr =
- query.GetObjectDescr(type_map, object_id, true);
- if (!obj_descr.is_object || obj_descr.id <= 0) {
- return CRef<CSeq_entry>();
- }
- CNcbiIfstream in(obj_descr.file_name.c_str(),
- IOS_BASE::in | IOS_BASE::binary);
- if (!in.is_open()) {
- string msg = "Cannot open file:";
- msg.append(obj_descr.file_name);
- LDS_THROW(eFileNotFound, msg);
- }
- switch (obj_descr.format) {
- case CFormatGuess::eFasta:
- return ReadFasta(in, fReadFasta_AssumeNuc);
- case CFormatGuess::eTextASN:
- case CFormatGuess::eXml:
- case CFormatGuess::eBinaryASN:
- {
- in.seekg(obj_descr.offset);
- auto_ptr<CObjectIStream>
- is(CObjectIStream::Open(FormatGuess2Serial(obj_descr.format), in));
- if (obj_descr.type_str == "Bioseq") {
- //
- // If object is a bare Bioseq: read it and
- // construct a Seq_entry on it
- //
- CRef<CBioseq> bioseq(new CBioseq());
- is->Read(ObjectInfo(*bioseq));
- CRef<CSeq_entry> seq_entry(new CSeq_entry());
- seq_entry->SetSeq(*bioseq);
- return seq_entry;
- } else
- if (obj_descr.type_str == "Seq-entry") {
- CRef<CSeq_entry> seq_entry(new CSeq_entry());
- is->Read(ObjectInfo(*seq_entry));
- return seq_entry;
- } else {
- LDS_THROW(eInvalidDataType, "Non Seq-entry object type");
- }
- }
- break;
- default:
- LDS_THROW(eNotImplemented, "Not implemeneted yet.");
- }
- }
- CRef<CSeq_annot> LDS_LoadAnnot(SLDS_TablesCollection& lds_db,
- const CLDS_Query::SObjectDescr& obj_descr)
- {
- CNcbiIfstream in(obj_descr.file_name.c_str(),
- IOS_BASE::in | IOS_BASE::binary);
- if (!in.is_open()) {
- string msg = "Cannot open file:";
- msg.append(obj_descr.file_name);
- LDS_THROW(eFileNotFound, msg);
- }
- switch (obj_descr.format) {
- case CFormatGuess::eTextASN:
- case CFormatGuess::eXml:
- case CFormatGuess::eBinaryASN:
- {
- in.seekg(obj_descr.offset);
- auto_ptr<CObjectIStream>
- is(CObjectIStream::Open(FormatGuess2Serial(obj_descr.format), in));
- if (obj_descr.type_str == "Seq-annot") {
- //
- // If object is a bare Bioseq: read it and
- // construct a Seq_entry on it
- //
- CRef<CSeq_annot> annot(new CSeq_annot());
- is->Read(ObjectInfo(*annot));
- return annot;
- } else
- if (obj_descr.type_str == "Seq-align") {
- CRef<CSeq_align> align(new CSeq_align());
- is->Read(ObjectInfo(*align));
- CRef<CSeq_annot> annot(new CSeq_annot());
- annot->SetData().SetAlign().push_back(align);
- return annot;
- } else {
- LDS_THROW(eInvalidDataType,
- "Non Seq-aanot compatible object type");
- }
- }
- break;
- default:
- LDS_THROW(eNotImplemented, "Invalid file format");
- }
-
- }
- END_SCOPE(objects)
- END_NCBI_SCOPE
- /*
- * ===========================================================================
- * $Log: lds_reader.cpp,v $
- * Revision 1000.1 2004/06/01 19:45:52 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
- *
- * Revision 1.6 2004/05/21 21:42:55 gorelenk
- * Added PCH ncbi_pch.hpp
- *
- * Revision 1.5 2003/07/14 19:47:01 kuznets
- * + new annotation reader
- *
- * Revision 1.4 2003/07/10 20:10:09 kuznets
- * Code clean up
- *
- * Revision 1.3 2003/06/23 18:57:31 kuznets
- * LDS_LoadTSE corrected to read XML serialization format.
- *
- * Revision 1.2 2003/06/09 18:06:33 kuznets
- * CSeq_entry reader changed to handle top level CBioseqs.
- *
- * Revision 1.1 2003/06/06 20:02:34 kuznets
- * Initial revision
- *
- *
- * ===========================================================================
- */
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