local_db_adapter.hpp

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/* $Id: local_db_adapter.hpp 87240 2019-08-12 11:18:21Z fongah2 $
 * ===========================================================================
 *
 *                            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    
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 *  thus cannot be copyrighted.  This software/database is freely available 
 *  to the public for use. The National Library of Medicine and the U.S.    
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 * ===========================================================================
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 * Author: Christiam Camacho
 *
 */
 
/** @file local_db_adapter.hpp
 * Declares class which provides internal BLAST database representations to the
 * internal BLAST APIs
 */
 
#ifndef ALGO_BLAST_API___LOCAL_DB_ADAPTER_HPP
#define ALGO_BLAST_API___LOCAL_DB_ADAPTER_HPP
 
#include <algo/blast/core/blast_seqsrc.h>
#include <algo/blast/api/uniform_search.hpp> // for CSearchDatabase
#include <objtools/blast/seqdb_reader/seqdb.hpp>  // for CSeqDB
#include <algo/blast/api/sseqloc.hpp>        // for TSeqLocVector
 
/** @addtogroup AlgoBlast
 *
 * @{
 */
 
// Forward declaration
struct BlastSeqSrc;
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(blast)
 
// Forward declaration
class IBlastSeqInfoSrc;
 
/// Interface to create a BlastSeqSrc suitable for use in CORE BLAST from a
/// a variety of BLAST database/subject representations
class NCBI_XBLAST_EXPORT CLocalDbAdapter : public CObject
{
public:
    /// Constructor
    /// @param dbinfo 
    ///     Description of BLAST database
    CLocalDbAdapter(const CSearchDatabase& dbinfo);
    
    /// Constructor
    /// @param subject_sequences
    ///     Set of sequences which should be used as subjects
    /// @param opts_handle
    ///     Options to be used (needed to create the ILocalQueryData)
    /// @param dbscan_mode Database search mode (as opposed to pairwise)
    CLocalDbAdapter(CRef<IQueryFactory> subject_sequences,
                    CConstRef<CBlastOptionsHandle> opts_handle,
            bool dbscan_mode=false);
 
    /// Constructor taking custom BlastSeqSrc and IBlastSeqInfoSrc objects
    /// @param seqSrc 
    ///     Custom BlastSeqSrc implementation provided by the user
    /// @param seqInfoSrc
    ///     Custom IBlastSeqInfoSrc implementation provided by the user
    CLocalDbAdapter(BlastSeqSrc* seqSrc,
                    CRef<IBlastSeqInfoSrc> seqInfoSrc);
 
    /// Destructor
    virtual ~CLocalDbAdapter();
 
    /// This method should be called so that if the implementation has an
    /// internal "bookmark" of the chunks of the database it has assigned to
    /// different threads, this can be reset at the start of a PSI-BLAST
    /// iteration (or when reusing the same object to iterate over the 
    /// database/subjects when the query is split).
    /// This method should be called before calling MakeSeqSrc() to
    /// ensure proper action on retrieving the BlastSeqSrc (in some cases it
    /// might cause a re-construction of the underlying BlastSeqSrc
    /// implementation). Note that in some cases, this operation might not apply
    void ResetBlastSeqSrcIteration();
 
    /// Retrieves or constructs the BlastSeqSrc
    /// @note ownership of the constructed object is handled by this class
    BlastSeqSrc* MakeSeqSrc();
 
    /// Retrieves or constructs the IBlastSeqInfoSrc
    /// @note ownership of the constructed object is handled by this class
    IBlastSeqInfoSrc* MakeSeqInfoSrc();
 
    /// Retrieve the database filtering algorithm
    /// @returns -1 if not none was used, otherwise the filtering algorithm ID
    int GetFilteringAlgorithm();
 
    /// Retrieve the database filtering id from key
    /// @returns kEmptyStr if not none was found, otherwise the filtering algorithm key
    string GetFilteringAlgorithmKey();
 
 
    /// Returns true if this object represents protein or nucleotide sequences
    bool IsProtein() const;
 
    /// Returns the database name if appropriate, else kEmptyStr for subject
    /// sequences
    string GetDatabaseName() const { return m_DbName; }
    
    /// Returns true if this object represents a BLAST database
    bool IsBlastDb() const { return m_DbName != kEmptyStr; }
 
    /// Returns true if this is not a database but is database scanning mode
    bool IsDbScanMode() const { return m_DbScanMode; }
 
    CRef<CSearchDatabase> GetSearchDatabase() {return m_DbInfo;}
private:
    /// Pointer to the BlastSeqSrc this object owns and manages
    BlastSeqSrc* m_SeqSrc;
 
    /// Pointer to the IBlastSeqInfoSrc
    CRef<IBlastSeqInfoSrc> m_SeqInfoSrc;
 
    /// Object containing BLAST database description
    CRef<CSearchDatabase> m_DbInfo;
 
    /// IQueryFactory containing the subject sequences
    CRef<IQueryFactory> m_SubjectFactory;
 
    /// Options to be used when instantiating the subject sequences
    CConstRef<CBlastOptionsHandle> m_OptsHandle;
 
    /// This is initialized ONLY if the m_SubjectFactory is of type
    /// CObjMgr_QueryFactory, case in which it's not empty. This is needed to
    /// handle delta sequences as input and it uses the object manager APIs
    TSeqLocVector m_Subjects;
 
    /// This is initialized ONLY if this object represents a BLAST database
    const string m_DbName;
 
    /// Specifies that bl2seq search run in database scan mode (not pairwise)
    bool m_DbScanMode;
    
    /// Prohibit copy-constructor
    CLocalDbAdapter(const CLocalDbAdapter&);
    /// Prohibit assignment operator
    CLocalDbAdapter & operator=(const CLocalDbAdapter&);
};
 
inline int
CLocalDbAdapter::GetFilteringAlgorithm() 
{
    return (m_DbInfo.Empty() ? -1 : m_DbInfo->GetFilteringAlgorithm());
}
 
END_SCOPE(BLAST)
END_NCBI_SCOPE
 
/* @} */
 
#endif /* ALGO_BLAST_API___LOCAL_DB_ADAPTER__HPP */