seq_id_tree.hpp

ncbi源码

class CSeq_id_GB_Tree : public CSeq_id_Textseq_Tree
{
protected:
    virtual bool x_Check(const CSeq_id& id) const;
    virtual const CTextseq_id& x_Get(const CSeq_id& id) const;
};


////////////////////////////////////////////////////////////////////
// Pir tree


class CSeq_id_Pir_Tree : public CSeq_id_Textseq_Tree
{
protected:
    virtual bool x_Check(const CSeq_id& id) const;
    virtual const CTextseq_id& x_Get(const CSeq_id& id) const;
};


////////////////////////////////////////////////////////////////////
// Swissprot


class CSeq_id_Swissprot_Tree : public CSeq_id_Textseq_Tree
{
protected:
    virtual bool x_Check(const CSeq_id& id) const;
    virtual const CTextseq_id& x_Get(const CSeq_id& id) const;
};


////////////////////////////////////////////////////////////////////
// Prf tree


class CSeq_id_Prf_Tree : public CSeq_id_Textseq_Tree
{
protected:
    virtual bool x_Check(const CSeq_id& id) const;
    virtual const CTextseq_id& x_Get(const CSeq_id& id) const;
};


////////////////////////////////////////////////////////////////////
// Tpg tree


class CSeq_id_Tpg_Tree : public CSeq_id_Textseq_Tree
{
protected:
    virtual bool x_Check(const CSeq_id& id) const;
    virtual const CTextseq_id& x_Get(const CSeq_id& id) const;
};


////////////////////////////////////////////////////////////////////
// Tpe tree


class CSeq_id_Tpe_Tree : public CSeq_id_Textseq_Tree
{
protected:
    virtual bool x_Check(const CSeq_id& id) const;
    virtual const CTextseq_id& x_Get(const CSeq_id& id) const;
};


////////////////////////////////////////////////////////////////////
// Tpd tree


class CSeq_id_Tpd_Tree : public CSeq_id_Textseq_Tree
{
protected:
    virtual bool x_Check(const CSeq_id& id) const;
    virtual const CTextseq_id& x_Get(const CSeq_id& id) const;
};


////////////////////////////////////////////////////////////////////
// Other tree


class CSeq_id_Other_Tree : public CSeq_id_Textseq_Tree
{
protected:
    virtual bool x_Check(const CSeq_id& id) const;
    virtual const CTextseq_id& x_Get(const CSeq_id& id) const;
};


////////////////////////////////////////////////////////////////////
// e_Local tree


class CSeq_id_Local_Tree : public CSeq_id_Which_Tree
{
public:
    CSeq_id_Local_Tree(void);
    ~CSeq_id_Local_Tree(void);

    virtual bool Empty(void) const;

    virtual CSeq_id_Handle FindInfo(const CSeq_id& id) const;
    virtual CSeq_id_Handle FindOrCreate(const CSeq_id& id);

    virtual bool HaveMatch(const CSeq_id_Handle& id) const;
    virtual void FindMatch(const CSeq_id_Handle& id,
                           TSeq_id_MatchList& id_list) const;
    virtual void FindMatchStr(string sid,
                              TSeq_id_MatchList& id_list) const;

private:
    virtual void x_Unindex(const CSeq_id_Info* info);
    CSeq_id_Info* x_FindInfo(const CObject_id& oid) const;

    typedef map<string, CSeq_id_Info*, PNocase> TByStr;
    typedef map<int, CSeq_id_Info*>    TById;

    TByStr m_ByStr;
    TById  m_ById;
};


////////////////////////////////////////////////////////////////////
// e_General tree


class CSeq_id_General_Tree : public CSeq_id_Which_Tree
{
public:
    CSeq_id_General_Tree(void);
    ~CSeq_id_General_Tree(void);

    virtual bool Empty(void) const;

    virtual CSeq_id_Handle FindInfo(const CSeq_id& id) const;
    virtual CSeq_id_Handle FindOrCreate(const CSeq_id& id);

    virtual bool HaveMatch(const CSeq_id_Handle& id) const;
    virtual void FindMatch(const CSeq_id_Handle& id,
                           TSeq_id_MatchList& id_list) const;
    virtual void FindMatchStr(string sid,
                              TSeq_id_MatchList& id_list) const;

private:
    virtual void x_Unindex(const CSeq_id_Info* info);
    CSeq_id_Info* x_FindInfo(const CDbtag& dbid) const;

    struct STagMap {
    public:
        typedef map<string, CSeq_id_Info*, PNocase> TByStr;
        typedef map<int, CSeq_id_Info*>    TById;

        TByStr m_ByStr;
        TById  m_ById;
    };
    typedef map<string, STagMap, PNocase> TDbMap;

    TDbMap m_DbMap;
};


////////////////////////////////////////////////////////////////////
// e_Giim tree


class CSeq_id_Giim_Tree : public CSeq_id_Which_Tree
{
public:
    CSeq_id_Giim_Tree(void);
    ~CSeq_id_Giim_Tree(void);

    virtual bool Empty(void) const;

    virtual CSeq_id_Handle FindInfo(const CSeq_id& id) const;
    virtual CSeq_id_Handle FindOrCreate(const CSeq_id& id);

    virtual bool HaveMatch(const CSeq_id_Handle& ) const;
    virtual void FindMatch(const CSeq_id_Handle& id,
                           TSeq_id_MatchList& id_list) const;
    virtual void FindMatchStr(string sid,
                              TSeq_id_MatchList& id_list) const;

private:
    virtual void x_Unindex(const CSeq_id_Info* info);
    CSeq_id_Info* x_FindInfo(const CGiimport_id& gid) const;

    // 2-level indexing: first by Id, second by Db+Release
    typedef vector<CSeq_id_Info*> TGiimList;
    typedef map<int, TGiimList>  TIdMap;

    TIdMap m_IdMap;
};


////////////////////////////////////////////////////////////////////
// e_Patent tree


class CSeq_id_Patent_Tree : public CSeq_id_Which_Tree
{
public:
    CSeq_id_Patent_Tree(void);
    ~CSeq_id_Patent_Tree(void);

    virtual bool Empty(void) const;

    virtual CSeq_id_Handle FindInfo(const CSeq_id& id) const;
    virtual CSeq_id_Handle FindOrCreate(const CSeq_id& id);

    virtual bool HaveMatch(const CSeq_id_Handle& ) const;
    virtual void FindMatch(const CSeq_id_Handle& id,
                           TSeq_id_MatchList& id_list) const;
    virtual void FindMatchStr(string sid,
                              TSeq_id_MatchList& id_list) const;

private:
    virtual void x_Unindex(const CSeq_id_Info* info);
    CSeq_id_Info* x_FindInfo(const CPatent_seq_id& pid) const;

    // 3-level indexing: country, (number|app_number), seqid.
    // Ignoring patent doc-type in indexing.
    struct SPat_idMap {
        typedef map<int, CSeq_id_Info*> TBySeqid;
        typedef map<string, TBySeqid, PNocase> TByNumber; // or by App_number

        TByNumber m_ByNumber;
        TByNumber m_ByApp_number;
    };
    typedef map<string, SPat_idMap, PNocase> TByCountry;

    TByCountry m_CountryMap;
};


////////////////////////////////////////////////////////////////////
// e_PDB tree


class CSeq_id_PDB_Tree : public CSeq_id_Which_Tree
{
public:
    CSeq_id_PDB_Tree(void);
    ~CSeq_id_PDB_Tree(void);

    virtual bool Empty(void) const;

    virtual CSeq_id_Handle FindInfo(const CSeq_id& id) const;
    virtual CSeq_id_Handle FindOrCreate(const CSeq_id& id);

    virtual void FindMatch(const CSeq_id_Handle& id,
                           TSeq_id_MatchList& id_list) const;
    virtual void FindMatchStr(string sid,
                              TSeq_id_MatchList& id_list) const;

private:
    virtual void x_Unindex(const CSeq_id_Info* info);
    CSeq_id_Info* x_FindInfo(const CPDB_seq_id& pid) const;

    string x_IdToStrKey(const CPDB_seq_id& id) const;

    // Index by mol+chain, no date - too complicated
    typedef vector<CSeq_id_Info*>  TSubMolList;
    typedef map<string, TSubMolList, PNocase> TMolMap;

    TMolMap m_MolMap;
};



/////////////////////////////////////////////////////////////////////////////
//
// Inline methods
//
/////////////////////////////////////////////////////////////////////////////

END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: seq_id_tree.hpp,v $
* Revision 1000.1  2004/04/12 17:28:34  gouriano
* PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.5
*
* Revision 1.5  2004/02/19 17:25:34  vasilche
* Use CRef<> to safely hold pointer to CSeq_id_Info.
* CSeq_id_Info holds pointer to owner CSeq_id_Which_Tree.
* Reduce number of calls to CSeq_id_Handle.GetSeqId().
*
* Revision 1.4  2004/02/10 21:15:15  grichenk
* Added reverse ID matching.
*
* Revision 1.3  2004/01/08 02:49:11  ucko
* Make m_TreeLock a recursive mutex, as CSeq_id_Textseq_Tree can no
* longer safely use a fast mutex.
*
* Revision 1.2  2003/09/30 16:22:01  vasilche
* Updated internal object manager classes to be able to load ID2 data.
* SNP blobs are loaded as ID2 split blobs - readers convert them automatically.
* Scope caches results of requests for data to data loaders.
* Optimized CSeq_id_Handle for gis.
* Optimized bioseq lookup in scope.
* Reduced object allocations in annotation iterators.
* CScope is allowed to be destroyed before other objects using this scope are
* deleted (feature iterators, bioseq handles etc).
* Optimized lookup for matching Seq-ids in CSeq_id_Mapper.
* Added 'adaptive' option to objmgr_demo application.
*
* Revision 1.1  2003/06/10 19:06:35  vasilche
* Simplified CSeq_id_Mapper and CSeq_id_Handle.
*
*
* ===========================================================================
*/

#endif  /* OBJECTS_OBJMGR___SEQ_ID_TREE__HPP */