NCBI C++ Toolkit Cross Reference


#ifndef NGALIGN_INVERSION_MERGE_ALIGNER__HPP #define NGALIGN_INVERSION_MERGE_ALIGNER__HPP /* $Id: inversion_merge_aligner.hpp 47096 2010-09-10 16:21:43Z 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: Nathan Bouk * * File Description: * */ #include <corelib/ncbistd.hpp> #include <corelib/ncbiobj.hpp> #include <objects/seqloc/Na_strand.hpp> #include <objects/seqloc/Seq_loc.hpp> #include <objects/seqloc/Seq_id.hpp> #include <objmgr/scope.hpp> #include <algo/blast/api/blast_types.hpp> #include <algo/blast/api/bl2seq.hpp> #include <algo/blast/api/blast_options_handle.hpp> #include <algo/blast/api/blast_nucl_options.hpp> #include <objects/seqalign/Seq_align.hpp> #include <objects/seqalign/Seq_align_set.hpp> #include <objects/seqalign/Dense_seg.hpp> #include <algo/align/ngalign/ngalign_interface.hpp> BEGIN_NCBI_SCOPE BEGIN_SCOPE(objects) class CScope; class CSeq_align; class CSeq_align_set; class CSeq_id; class CDense_seg; END_SCOPE(objects) class CInversionMergeAligner : public IAlignmentFactory { public: CInversionMergeAligner(int Threshold) : m_Threshold(Threshold) { ; } string GetName() const { return "inversion_merge_aligner"; } TAlignResultsRef GenerateAlignments(objects::CScope& Scope, ISequenceSet* QuerySet, ISequenceSet* SubjectSet, TAlignResultsRef AccumResults); static bool s_SortByPctCoverage(const CRef<objects::CSeq_align>& A, const CRef<objects::CSeq_align>& B); protected: private: int m_Threshold; void x_RunMerger(objects::CScope& Scope, CQuerySet& QueryAligns, TAlignResultsRef Results); void x_SortAlignSet(objects::CSeq_align_set& AlignSet); void x_SplitAlignmentsByStrand(const objects::CSeq_align_set& Source, objects::CSeq_align_set& Pluses, objects::CSeq_align_set& Minuses); void x_HandleSingleStrandMerging(objects::CSeq_align_set& Source, objects::CSeq_align_set& Results, objects::CScope& Scope); CRef<objects::CSeq_align> x_CreateDiscAlignment(const objects::CSeq_align& Dom, const objects::CSeq_align& Non, objects::CScope& Scope); CRef<objects::CSeq_align_set> x_MergeSeqAlignSet(const objects::CSeq_align_set& InAligns, objects::CScope& Scope); bool x_IsAllGap(const objects::CDense_seg& Denseg); }; END_NCBI_SCOPE #endif

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