gff_reader.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: gff_reader.hpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 19:40:36  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
 * PRODUCTION
 * ===========================================================================
 */

#ifndef OBJTOOLS_READERS___GFF_READER__HPP
#define OBJTOOLS_READERS___GFF_READER__HPP

/*  $Id: gff_reader.hpp,v 1000.1 2004/06/01 19:40:36 gouriano Exp $
 * ===========================================================================
 *
 *                            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:  Aaron Ucko, Wratko Hlavina
 *
 */

/// @file gff_reader.hpp
/// Reader for GFF (including GTF) files.
///
/// These formats are somewhat loosely defined (for the record, at
/// http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml and
/// http://genes.cs.wustl.edu/GTF2.html respectively).  As such, the
/// reader allows heavy application-specific tuning, both via flags
/// and via virtual methods.


#include <corelib/ncbiutil.hpp>
#include <util/range_coll.hpp>

#include <objects/seq/Bioseq.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqset/Seq_entry.hpp>

#include <objtools/readers/reader_exception.hpp>

#include <set>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)


/** @addtogroup Miscellaneous
 *
 * @{
 */

class NCBI_XOBJREAD_EXPORT CGFFReader
{
public:
    enum EFlags {
        fNoGTF      = 0x1, // don't honor/recognize GTF conventions
        fGBQuals    = 0x2, // attribute tags are GenBank qualifiers
        fMergeExons = 0x4  // merge exons with the same transcript_id
    };
    typedef int TFlags;

    virtual ~CGFFReader() { }

    CRef<CSeq_entry> Read(CNcbiIstream& in, TFlags flags = 0);

    struct SRecord : public CObject
    {
        struct SSubLoc
        {
            string         accession;
            ENa_strand     strand;
            set<TSeqRange> ranges;
        };

        typedef set<vector<string> > TAttrs;
        typedef vector<SSubLoc>      TLoc;

        TLoc         loc;       ///< from accession, start, stop, strand
        string       source;
        string       key;
        string       score;
        int          frame;     ///< 0-based; . maps to -1.
        TAttrs       attrs;
        unsigned int line_no;

        TAttrs::const_iterator FindAttribute(const string& name,
                                             size_t min_values = 1) const;
    };

protected:
    virtual void            x_Warn(const string& message,
                                   unsigned int line = 0);

    /// Reset all state, since we're between streams.
    virtual void            x_Reset(void);

    TFlags                  x_GetFlags(void) const { return m_Flags; }
    bool                    x_GetNextLine(string& line);
    unsigned int            x_GetLineNumber(void) { return m_LineNumber; }

    virtual void            x_ParseStructuredComment(const string& line);
    virtual void            x_ParseDateComment(const string& date);
    virtual void            x_ParseTypeComment(const string& moltype,
                                               const string& seqname);

    virtual CRef<SRecord>   x_ParseFeatureInterval(const string& line);
    virtual CRef<SRecord>   x_NewRecord(void)
        { return CRef<SRecord>(new SRecord); }
    virtual CRef<CSeq_feat> x_ParseRecord(const SRecord& record);
    virtual CRef<CSeq_loc>  x_ResolveLoc(const SRecord::TLoc& loc);
    virtual void            x_AddAttribute(SRecord& record,
                                           vector<string>& attr);

    /// Returning the empty string indicates that record constitutes
    /// an entire feature.  Returning anything else requests merging
    /// with other records that yield the same ID.
    virtual string          x_FeatureID(const SRecord& record);

    virtual void            x_MergeRecords(SRecord& dest, const SRecord& src);
    virtual void            x_MergeAttributes(SRecord& dest,
                                              const SRecord& src);
    virtual void            x_PlaceFeature(CSeq_feat& feat,
                                           const SRecord& record);

    /// Falls back to x_ResolveNewSeqName on cache misses.
    virtual CRef<CSeq_id>   x_ResolveSeqName(const string& name);

    virtual CRef<CSeq_id>   x_ResolveNewSeqName(const string& name);

    /// Falls back to x_ResolveNewID on cache misses.
    virtual CRef<CBioseq>   x_ResolveID(const CSeq_id& id, const string& mol);

    /// The base version just constructs a shell so as not to depend
    /// on the object manager, but derived versions may consult it.
    virtual CRef<CBioseq>   x_ResolveNewID(const CSeq_id& id,
                                           const string& mol);

    virtual void            x_PlaceSeq(CBioseq& seq);

private:
    typedef map<string, CRef<CSeq_id>, PNocase>    TSeqNameCache;
    typedef map<CConstRef<CSeq_id>, CRef<CBioseq>,
                PPtrLess<CConstRef<CSeq_id> > >    TSeqCache;
    typedef map<string, CRef<SRecord>, PNocase>    TDelayedFeats;

    CRef<CSeq_entry> m_TSE;
    TSeqNameCache    m_SeqNameCache;
    TSeqCache        m_SeqCache;
    TDelayedFeats    m_DelayedFeats;
    string           m_DefMol;
    unsigned int     m_LineNumber;
    TFlags           m_Flags;
    CNcbiIstream*    m_Stream;
};


END_SCOPE(objects)
END_NCBI_SCOPE


/* @} */


/*
 * ===========================================================================
 * $Log: gff_reader.hpp,v $
 * Revision 1000.1  2004/06/01 19:40:36  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
 *
 * Revision 1.4  2004/05/08 12:14:16  dicuccio
 * Use set<TRange> instead of CRangeCollection<>
 *
 * Revision 1.3  2004/01/27 17:12:34  ucko
 * Make SRecord public to resolve visibility errors on IBM VisualAge C++.
 *
 * Revision 1.2  2003/12/03 21:03:19  ucko
 * Add Windows export specifier.
 *
 * Revision 1.1  2003/12/03 20:56:19  ucko
 * Initial commit.
 *
 * ===========================================================================
 */

#endif  /* OBJTOOLS_READERS___GFF_READER__HPP */