NCBI C++ Toolkit Cross Reference


/* $Id: psiblast_aux_priv.hpp 41998 2009-05-27 17:35:47Z camacho $ * =========================================================================== * * 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: Christiam Camacho * */ /** @file psiblast_aux_priv.hpp * Declarations of auxiliary functions/classes for PSI-BLAST */ #ifndef ALGO_BLAST_API___PSIBLAST_AUX_PRIV__HPP #define ALGO_BLAST_API___PSIBLAST_AUX_PRIV__HPP #include <corelib/ncbiobj.hpp> #include <objects/seqalign/Dense_seg.hpp> #include <algo/blast/core/blast_export.h> #include <algo/blast/api/psiblast_iteration.hpp> /** @addtogroup AlgoBlast * * @{ */ struct BlastScoreBlk; struct PSIBlastOptions; BEGIN_NCBI_SCOPE ///////////////////////////////////////////////////////////////////////////// // Forward declarations template <class T> class CNcbiMatrix; BEGIN_SCOPE(objects) class CSeq_id; class CBioseq; class CSeq_align_set; class CPssmWithParameters; END_SCOPE(objects) BEGIN_SCOPE(blast) class CBlastOptions; class CBlastOptionsHandle; class IQueryFactory; class TSearchMessages; ///////////////////////////////////////////////////////////////////////////// // Function prototypes/Class definitions /** Setup CORE BLAST score block structure with data from the scoremat PSSM. * @note this function might modify the composition based statistics settings. * @param score_blk BlastScoreBlk structure to set up [in|out] * @param pssm scoremat PSSM [in] * @param messages Error/warning messages [in|out] * @param options PSI-BLAST options [in|out] */ void NCBI_XBLAST_EXPORT PsiBlastSetupScoreBlock(BlastScoreBlk* score_blk, CConstRef<objects::CPssmWithParameters> pssm, TSearchMessages& messages, CConstRef<CBlastOptions> options); /** Given a PSSM with frequency ratios and options, invoke the PSSM engine to * compute the scores. * @param pssm object containing the PSSM's frequency ratios [in|out] * @param opts PSSM engine options [in] */ void NCBI_XBLAST_EXPORT PsiBlastComputePssmScores(CRef<objects::CPssmWithParameters> pssm, const CBlastOptions& opts); /// Returns the lowest score from the list of scores in CDense_seg::TScores /// @param scores list of scores [in] /// @param bit_score If not NULL, returns the bit score corresponding to the /// lowest evalue found [in|out] double NCBI_XBLAST_EXPORT GetLowestEvalue(const objects::CDense_seg::TScores& scores, double* bit_score = NULL); /** Auxiliary class to retrieve sequence identifiers its position in the * alignment which are below the inclusion evalue threshold. */ class NCBI_XBLAST_EXPORT CPsiBlastAlignmentProcessor { public: /// Container of Seq-ids for the subject sequences (hits) aligned with the /// query typedef CPsiBlastIterationState::TSeqIds THitIdentifiers; /// Extract all the THitId which have evalues below the inclusion threshold /// @param alignments /// alignments corresponding to one query sequence [in] /// @param evalue_inclusion_threshold /// All hits in the above alignment which have evalues below this /// parameter will be included in the return value [in] /// @param output /// Return value of this method [out] void operator()(const objects::CSeq_align_set& alignments, double evalue_inclusion_threshold, THitIdentifiers& output); }; /// Auxialiry class containing static methods to validate PSI-BLAST search /// components class NCBI_XBLAST_EXPORT CPsiBlastValidate { public: /** Perform validation on the PSSM * @param pssm PSSM as specified in scoremat.asn [in] * @param require_scores Set to true if scores MUST be present (otherwise, * either scores or frequency ratios are acceptable) [in] * @throws CBlastException on failure when validating data */ static void Pssm(const objects::CPssmWithParameters& pssm, bool require_scores = false); /// Enumeration to specify the different uses of the query factory enum EQueryFactoryType { eQFT_Query, eQFT_Subject }; /// Function to perform sanity checks on the query factory static void QueryFactory(CRef<IQueryFactory> query_factory, const CBlastOptionsHandle& opts_handle, EQueryFactoryType query_factory_type = eQFT_Query); }; /** Even though the query sequence and the matrix gap costs are not a * product of the PSSM engine, set them as they are required for the * PSI-BLAST (query sequence) and RPS-BLAST/formatrpsdb (gap costs) * @param pssm PSSM to modify [in|out] * @param gap_open Gap opening cost associated with the matrix used to build * the PSSM [in] * @param gap_extend Gap extension cost associated with the matrix used to * build the PSSM [in] */ NCBI_XBLAST_EXPORT void PsiBlastAddAncillaryPssmData(objects::CPssmWithParameters& pssm, int gap_open, int gap_extend); END_SCOPE(blast) END_NCBI_SCOPE /* @} */ #endif /* ALGO_BLAST_API___PSIBLAST_AUX_PRIV__HPP */

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