NCBI C++ Toolkit Cross Reference


#ifndef ALGO_COBALT___COBALT_APP_UTIL__HPP #define ALGO_COBALT___COBALT_APP_UTIL__HPP /* $Id: cobalt_app_util.hpp 51015 2011-08-25 15:03:46Z boratyng $ * =========================================================================== * * 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 offical 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. * * ===========================================================================*/ /***************************************************************************** File name: cobalt_app_util.hpp Author: Greg Boratyn Contents: Utility functions for COBALT command line applications ******************************************************************************/ #include <objects/seqalign/Seq_align.hpp> #include <objmgr/object_manager.hpp> #include <objmgr/util/sequence.hpp> #include <objtools/readers/fasta.hpp> BEGIN_NCBI_SCOPE BEGIN_SCOPE(cobalt) /// Reads fasta sequences from stream, adds them to scope, /// and returns them as the list of Seq_locs /// @param instream Input Stream [in|out] /// @param seqs List of the read sequences [out] /// @param scope Scope that contains the read sequences [in|out] /// @param flags Fasta Reader flags [in] void GetSeqLocFromStream(CNcbiIstream& instream, vector< CRef<objects::CSeq_loc> >& seqs, CRef<objects::CScope>& scope, objects::CFastaReader::TFlags flags); /// Reads fasta sequences as multiple sequence alignment /// @param instream Input stream [in|out] /// @param scope Scope that contains the read sequences [in|out] /// @param flags Fasta Reader flags [in] /// @param id_generator Generator for sequece ids [in|out] /// @return Alignment in ASN.1 format CRef<objects::CSeq_align> GetAlignmentFromStream(CNcbiIstream& instream, CRef<objects::CScope>& scope, objects::CFastaReader::TFlags flags, objects::CSeqIdGenerator& id_generator); END_SCOPE(cobalt) END_NCBI_SCOPE #endif /* ALGO_COBALT___COBALT_APP_UTIL_HPP */

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