blastdb_dataextract.hpp

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/*  $Id: blastdb_dataextract.hpp 100517 2023-08-09 13:02:28Z 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
 *  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 blastdb_dataextract.hpp
 *  Declares classes which extract data from a BLAST database
 */
 
#ifndef OBJTOOLS_BLASTDB_FORMAT___BLASTDB_DATAEXTRACT__HPP
#define OBJTOOLS_BLASTDB_FORMAT___BLASTDB_DATAEXTRACT__HPP
 
#include <objtools/blast/blastdb_format/blastdb_seqid.hpp>
#include <objtools/blast/seqdb_reader/seqdb.hpp>
#include <objmgr/util/sequence.hpp>
#include <sstream>
 
// Note: move this to corelib and define properly (see blastformat equivalent)
// #define NCBI_BLASTDB_FORMAT_EXPORT
 
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
 
/// Class to extract data from a BLAST database given an identifier
class NCBI_BLASTDB_FORMAT_EXPORT CBlastDBExtractor {
 
public:
    /// ctor
    CBlastDBExtractor(CSeqDB&             blastdb,
                      TSeqRange           range = TSeqRange(),
                      objects::ENa_strand strand = objects::eNa_strand_both,
                      int                 filt_algo_id = -1,
                      int                 fmt_algo_id = -1,
                      int                 line_width = 80,
                      bool                target_only = true,
                      bool                ctrl_a = false)
            : m_BlastDb(blastdb),
              m_OrigSeqRange(range),
              m_SeqRange(range),
              m_Strand(strand),
              m_FiltAlgoId(filt_algo_id),
              m_FmtAlgoId(fmt_algo_id),
              m_LineWidth(line_width),
              m_TargetOnly(target_only),
              m_UseCtrlA(ctrl_a),
              m_Oid(0),
              m_UseLongSeqIds(false)
 
    {
        m_Gi2TaxidMap.first = -1;
        m_Gi2AccMap.first = -1;
        m_Gi2TitleMap.first = -1;
        m_Oid2Pig.first = -1;
        m_Gi2SeqIdMap.first = -1;
 
        CNcbiApplicationAPI* app = CNcbiApplicationAPI::Instance();
        if (app) {
            const CNcbiRegistry& registry = app->GetConfig();
            m_UseLongSeqIds = (registry.Get("BLAST", "LONG_SEQID") == "1");
        }
    }
 
    /// Setting seqid
    /// @param id sequence identifier [in]
    void SetSeqId(const CBlastDBSeqId &seq_id, bool get_data = false);
    string ExtractOid();
    string ExtractPig();
    string ExtractGi();
    string ExtractAccession();
    string ExtractSeqId();
    string ExtractTitle();
    string ExtractTaxId();
    string ExtractLeafTaxIds();
    string ExtractCommonTaxonomicName();
    string ExtractLeafCommonTaxonomicNames();
    string ExtractScientificName();
    string ExtractLeafScientificNames();
    string ExtractBlastName();
    string ExtractSuperKingdom();
    string ExtractMaskingData();
    string ExtractSeqData();
    string ExtractSeqLen();
    string ExtractHash();
    string ExtractLinksInteger();
    string ExtractMembershipInteger();
    string ExtractAsn1Defline();
    string ExtractAsn1Bioseq();
    string ExtractFasta(const CBlastDBSeqId &seq_id);
 
    // Call before ExtractFasta or SetSeqId
    void SetConfig(TSeqRange range, objects::ENa_strand strand, int filt_algo_id);
 
protected:
    /// underlying Blast database
    CSeqDB& m_BlastDb;
    /// sequence range
    TSeqRange m_OrigSeqRange;
    /// sequence range
    TSeqRange m_SeqRange;
    /// strand
    objects::ENa_strand m_Strand;
    /// filtering algorithsm for sequence
    int m_FiltAlgoId;
    /// filtering algorithsm for outfmt
    int m_FmtAlgoId;
    /// FASTA output line width
    int m_LineWidth;
    /// Should the record contain mutilple seqids? (used only with %f)
    bool m_TargetOnly;
    /// Replace with ctrl_a? (used only with %f)
    bool m_UseCtrlA;
    typedef CSeqDB::TOID TOID;
    /// OID of the record
    TOID m_Oid;
    /// the target gi
    TGi m_Gi;
    /// bioseq
    CRef<CBioseq> m_Bioseq;
    /// Cache the defline (for membership bits)
    CRef<CBlast_def_line_set> m_Defline;
    /// Pair with a gi2taxid map for one Oid
    pair<TOID, map<TGi, TTaxId> > m_Gi2TaxidMap;
    /// Pair with a gi2taxid-set map for one Oid
    pair<TOID, map<TGi, set<TTaxId> > > m_Gi2TaxidSetMap;
    /// Pair with a gi2accesion map for one Oid
    pair<TOID, map<TGi, string> > m_Gi2AccMap;
    /// Pair with a gi2title map for one Oid
    pair<TOID, map<TGi, string> > m_Gi2TitleMap;
    /// Pair with a pig for one Oid.
    pair<TOID, CSeqDB::TPIG> m_Oid2Pig;
    // Pair with a gi2seqid for one Oid.
    pair<TOID, map<TGi, string> > m_Gi2SeqIdMap;
    /// Use long sequence ids (with gi and accessions with database source)
    bool m_UseLongSeqIds;
private:
    void x_ExtractMaskingData(CSeqDB::TSequenceRanges &ranges, int algo_id);
    TTaxId x_ExtractTaxId();
    void x_ExtractLeafTaxIds(set<TTaxId>& taxids);
    /// Sets the map
    void x_SetGi2AccMap();
    /// Sets the map
    void x_SetGi2TitleMap();
    // sets the gi to seqid map
    void x_SetGi2SeqIdMap();
 
    /// Initialize the cached defline
    void x_InitDefline();
 
    /// Setting the target_only m_Gi
    void x_SetGi();
};
 
class NCBI_BLASTDB_FORMAT_EXPORT CBlastDeflineUtil
{
public:
    struct BlastDeflineFields{
        unsigned int accession:1;
        unsigned int seq_id:1;
        unsigned int gi:1;
        unsigned int title:1;
        unsigned int membership:1;
        unsigned int tax_id:1;
        unsigned int leaf_node_tax_ids:1;
        // The tax names include: scientific_name, common_name, blast_name and super kingdom
        unsigned int tax_names:1;
        unsigned int leaf_node_tax_names:1;
        unsigned int pig:1;
        unsigned int links:1;
        unsigned int asn_defline:1;
 
    };
 
    enum FieldIndex {
        accession = 0,
        seq_id,
        gi,
        title,
        membership,
        pig,
        tax_id,
        leaf_node_tax_ids,
        scientific_name,
        leaf_node_scientific_names,
        common_name,
        leaf_node_common_names,
        blast_name,
        super_kingdom,
        links,
        asn_defline,
        max_index
    };
    static void ExtractDataFromBlastDeflineSet(const CBlast_def_line_set & dl_set,
                                               vector<string> & results,
                                               BlastDeflineFields fields,
                                               string target_id,
                                               bool use_long_id);
 
    static void ExtractDataFromBlastDefline(const CBlast_def_line & dl,
                                            vector<string> & results,
                                            BlastDeflineFields fields,
                                            bool use_long_id);
 
    static void ProcessFastaDeflines(CBioseq & bioseq,
                                     string & out,
                                     bool use_ctrla);
 
    static void ProcessFastaDeflines(CBioseq & bioseq,
                                     string & out,
                                     bool use_ctrla,
                                     const CSeq_loc* location,
                                     ENa_strand strand);
};
 
class NCBI_BLASTDB_FORMAT_EXPORT CBlastSeqUtil
{
public:
    static Uint4 GetSeqHash(const char* buffer, int length);
    static void ApplySeqMask(string & seq,
                             const CSeqDB::TSequenceRanges & masks,
                             const TSeqRange r=TSeqRange::GetEmpty());
    static void GetReverseStrandSeq(string & seq);
    static string GetMasksString(const CSeqDB::TSequenceRanges & masks);
 
};
 
END_NCBI_SCOPE
 
#endif /* OBJTOOLS_BLASTDB_FORMAT___BLASTDB_DATAEXTRACT__HPP */