NCBI C++ Toolkit Cross Reference


#ifndef __GLIMMER_READER__HPP #define __GLIMMER_READER__HPP /* $Id: glimmer_reader.hpp 40381 2008-12-10 19:43:19Z dicuccio $ * =========================================================================== * * 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 <corelib/ncbistd.hpp> #include <objmgr/scope.hpp> #include <objects/seqfeat/Genetic_code.hpp> BEGIN_NCBI_SCOPE class NCBI_XOBJREAD_EXPORT CGlimmerReader { public: CGlimmerReader(); /// read in and create a seq-annot for the glimmer input /// we also optionally create proteins for the CDSs /// we require a scope, as the genomes may be circular, and features /// crossing the origin cannot be placed without determining the length of /// the matched sequence. If the genetic code is not supplied, then it is /// assumed to be standard bacterial (code = 11) CRef<objects::CSeq_entry> Read(CNcbiIstream& istr, objects::CScope& scope, int genetic_code_idx = 11); }; END_NCBI_SCOPE #endif // __GLIMMER_READER__HPP

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