NCBI C++ Toolkit Cross Reference


/* $Id: su_sequence_set.hpp 33815 2007-05-04 17:18:18Z kazimird $ * =========================================================================== * * 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: Paul Thiessen * * File Description: * Classes to hold sets of sequences * * =========================================================================== */ #ifndef SU_SEQUENCE_SET__HPP #define SU_SEQUENCE_SET__HPP #include <corelib/ncbistd.hpp> #include <corelib/ncbistl.hpp> #include <corelib/ncbiobj.hpp> #include <string> #include <list> #include <objects/seqset/Seq_entry.hpp> #include <objects/seq/Bioseq.hpp> #include <objects/seqloc/Seq_id.hpp> BEGIN_SCOPE(struct_util) class NCBI_STRUCTUTIL_EXPORT Sequence : public ncbi::CObject { public: Sequence(ncbi::objects::CBioseq& bioseq); ~Sequence(void); ncbi::CRef < ncbi::objects::CBioseq > m_bioseqASN; std::string m_sequenceString, m_description; bool m_isProtein; unsigned int Length(void) const { return m_sequenceString.size(); } // Seq-id stuff const ncbi::objects::CSeq_id& GetPreferredIdentifier(void) const; const ncbi::objects::CBioseq::TId& GetAllIdentifiers(void) const { return m_bioseqASN->GetId(); } bool MatchesSeqId(const ncbi::objects::CSeq_id& seqID) const; std::string IdentifierString(void) const; }; class NCBI_STRUCTUTIL_EXPORT SequenceSet : public ncbi::CObject { public: typedef std::list < ncbi::CRef < ncbi::objects::CSeq_entry > > SeqEntryList; SequenceSet(SeqEntryList& seqEntries); typedef std::list < ncbi::CRef < Sequence > > SequenceList; SequenceList m_sequences; }; END_SCOPE(struct_util) #endif // SU_SEQUENCE_SET__HPP

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