flat_file_config.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: flat_file_config.hpp,v $
 * PRODUCTION Revision 1000.0  2004/06/01 19:48:19  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.2
 * PRODUCTION
 * ===========================================================================
 */

#ifndef OBJTOOLS_FORMAT___FLAT_FILE_CONFIG__HPP
#define OBJTOOLS_FORMAT___FLAT_FILE_CONFIG__HPP

/*  $Id: flat_file_config.hpp,v 1000.0 2004/06/01 19:48:19 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:  Mati Shomrat, NCBI
 *
 * File Description:
 *    Configuration class for flat-file generator
 */
#include <corelib/ncbistd.hpp>


BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)


// --- Flat File configuration class

class NCBI_FORMAT_EXPORT CFlatFileConfig
{
public:
    
    enum EFormat {
        // formatting styles    
        eFormat_GenBank,
        eFormat_EMBL,
        eFormat_DDBJ,
        eFormat_GBSeq,
        eFormat_FTable,
        eFormat_GFF
    };

    enum EMode {
        // determines the tradeoff between strictness and completeness
        eMode_Release = 0, // strict -- for official public releases
        eMode_Entrez,      // somewhat laxer -- for CGIs
        eMode_GBench,      // even laxer -- for editing submissions
        eMode_Dump         // shows everything, regardless of validity
    };


    enum EStyle {
        // determines handling of segmented records
        eStyle_Normal,  // default -- show segments iff they're near
        eStyle_Segment, // always show segments
        eStyle_Master,  // merge segments into a single virtual record
        eStyle_Contig   // just an index of segments -- no actual sequence
    };

    enum EFlags {
        // customization flags
        fDoHTML               = 0x1,
        fShowContigFeatures   = 0x2, // not just source features
        fShowContigSources    = 0x4, // not just focus
        fShowFarTranslations  = 0x8,
        fTranslateIfNoProduct = 0x10,
        fAlwaysTranslateCDS   = 0x20,
        fOnlyNearFeatures     = 0x40,
        fFavorFarFeatures     = 0x80,  // ignore near feats on segs w/far feats
        fCopyCDSFromCDNA      = 0x100, // for gen-prod sets
        fCopyGeneToCDNA       = 0x200, // for gen-prod sets
        fShowContigInMaster   = 0x400,
        fHideImpFeats         = 0x800,
        fHideRemoteImpFeats   = 0x1000,
        fHideSNPFeatures      = 0x2000,
        fHideExonFeatures     = 0x4000,
        fHideIntronFeatures   = 0x8000,
        fHideMiscFeatures     = 0x10000,
        fHideCDSProdFeatures  = 0x20000,
        fHideCDDFeats         = 0x40000,
        fShowTranscript       = 0x80000,
        fShowPeptides         = 0x100000,
        fHideGeneRIFs         = 0x200000,
        fOnlyGeneRIFs         = 0x400000,
        fLatestGeneRIFs       = 0x800000,
        fShowContigAndSeq     = 0x1000000,
        fHideSourceFeats      = 0x2000000,
        fShowFtableRefs       = 0x4000000,
        fOldFeatsOrder        = 0x8000000
    };

    enum EView {
        // determines which Bioseqs in an entry to view
        fViewNucleotides  = 0x1,
        fViewProteins     = 0x2,
        fViewAll          = (fViewNucleotides | fViewNucleotides)
    };

    // types
    typedef EFormat         TFormat;
    typedef EMode           TMode;
    typedef EStyle          TStyle;
    typedef unsigned int    TFlags; // binary OR of "EFlatFileFlags"
    typedef EView           TView;

    // constructors
    CFlatFileConfig(TFormat format = eFormat_GenBank,
                    TMode   mode = eMode_GBench,
                    TStyle  style = eStyle_Normal,
                    TFlags  flags = 0,
                    TView   view = fViewNucleotides);
    // destructor
    ~CFlatFileConfig(void);

    // -- Format
    // getters
    const TFormat& GetFormat(void) const { return m_Format; }
    bool IsFormatGenbank(void) const { return m_Format == eFormat_GenBank; }
    bool IsFormatEMBL   (void) const { return m_Format == eFormat_EMBL;    }
    bool IsFormatDDBJ   (void) const { return m_Format == eFormat_DDBJ;    }
    bool IsFormatGBSeq  (void) const { return m_Format == eFormat_GBSeq;   }
    bool IsFormatFTable (void) const { return m_Format == eFormat_FTable;  }
    bool IsFormatGFF    (void) const { return m_Format == eFormat_GFF;     }
    // setters
    void SetFormat(const TFormat& format) { m_Format = format; }
    void SetFormatGenbank(void) { m_Format = eFormat_GenBank; }
    void SetFormatEMBL   (void) { m_Format = eFormat_EMBL;    }
    void SetFormatDDBJ   (void) { m_Format = eFormat_DDBJ;    }
    void SetFormatGBSeq  (void) { m_Format = eFormat_GBSeq;   }
    void SetFormatFTable (void) { m_Format = eFormat_FTable;  }
    void SetFormatGFF    (void) { m_Format = eFormat_GFF;     }

    // -- Mode
    // getters
    const TMode& GetMode(void) const { return m_Mode; }
    bool IsModeRelease(void) const { return m_Mode == eMode_Release; }
    bool IsModeEntrez (void) const { return m_Mode == eMode_Entrez;  }
    bool IsModeGBench (void) const { return m_Mode == eMode_GBench;  }
    bool IsModeDump   (void) const { return m_Mode == eMode_Dump;    }
    // setters
    void SetMode(const TMode& mode) { m_Mode = mode; }
    void SetModeRelease(void) { m_Mode = eMode_Release; }
    void SetModeEntrez (void) { m_Mode = eMode_Entrez;  }
    void SetModeGBench (void) { m_Mode = eMode_GBench;  }
    void SetModeDump   (void) { m_Mode = eMode_Dump;    }

    // -- Style
    // getters
    const TStyle& GetStyle(void) const { return m_Style; }
    bool IsStyleNormal (void) const { return m_Style == eStyle_Normal;  }
    bool IsStyleSegment(void) const { return m_Style == eStyle_Segment; }
    bool IsStyleMaster (void) const { return m_Style == eStyle_Master;  }
    bool IsStyleContig (void) const { return m_Style == eStyle_Contig;  }
    // setters
    void SetStyle(const TStyle& style) { m_Style = style;  }
    void SetStyleNormal (void) { m_Style = eStyle_Normal;  }
    void SetStyleSegment(void) { m_Style = eStyle_Segment; }
    void SetStyleMaster (void) { m_Style = eStyle_Master;  }
    void SetStyleContig (void) { m_Style = eStyle_Contig;  }

    // -- View
    // getters
    const TView& GetView(void) const { return m_View; }
    bool IsViewNuc (void) const { return (m_View & fViewNucleotides) != 0; }
    bool IsViewProt(void) const { return (m_View & fViewProteins)    != 0; }
    bool IsViewAll (void) const { return IsViewNuc()  &&  IsViewProt();    }
    // setters
    void SetView(const TView& view) { m_View = view; }
    void SetViewNuc (void) { m_View = fViewNucleotides; }
    void SetViewProt(void) { m_View = fViewProteins;    }
    void SetViewAll (void) { m_View = fViewAll;         } 

    // -- Flags
    // getters
    const TFlags& GetFlags(void) const { return m_Flags; }
    // custumizable flags
    bool DoHTML              (void) const;
    bool HideImpFeats        (void) const;
    bool HideSNPFeatures     (void) const;
    bool HideExonFeatures    (void) const;
    bool HideIntronFeatures  (void) const;
    bool HideRemoteImpFeats  (void) const;
    bool HideGeneRIFs        (void) const;
    bool OnlyGeneRIFs        (void) const;
    bool HideCDSProdFeatures (void) const;
    bool HideCDDFeats        (void) const;
    bool LatestGeneRIFs      (void) const;
    bool ShowContigFeatures  (void) const;
    bool ShowContigSources   (void) const;
    bool ShowContigAndSeq    (void) const;
    bool CopyGeneToCDNA      (void) const;
    bool CopyCDSFromCDNA     (void) const;
    bool HideSourceFeats     (void) const;
    bool AlwaysTranslateCDS  (void) const;
    bool ShowFarTranslations (void) const;
    bool TranslateIfNoProduct(void) const;
    bool ShowTranscript      (void) const;
    bool ShowPeptides        (void) const;
    bool ShowFtableRefs      (void) const;
    bool OldFeatsOrder       (void) const;
    // mode dependant flags
    bool SuppressLocalId     (void) const;
    bool ValidateFeats       (void) const;
    bool IgnorePatPubs       (void) const;
    bool DropShortAA         (void) const;
    bool AvoidLocusColl      (void) const;
    bool IupacaaOnly         (void) const;
    bool DropBadCitGens      (void) const;
    bool NoAffilOnUnpub      (void) const;
    bool DropIllegalQuals    (void) const;
    bool CheckQualSyntax     (void) const;
    bool NeedRequiredQuals   (void) const;
    bool NeedOrganismQual    (void) const;
    bool NeedAtLeastOneRef   (void) const;
    bool CitArtIsoJta        (void) const;
    bool DropBadDbxref       (void) const;
    bool UseEmblMolType      (void) const;
    bool HideBankItComment   (void) const;
    bool CheckCDSProductId   (void) const;
    bool SuppressSegLoc      (void) const;
    bool SrcQualsToNote      (void) const;
    bool HideEmptySource     (void) const;
    bool GoQualsToNote       (void) const;
    bool GeneSynsToNote      (void) const;
    bool SelenocysteineToNote(void) const;
    bool ForGBRelease        (void) const;
    bool HideUnclassPartial  (void) const;
    
    // setters
    void SetFlags(const TFlags& flags) { m_Flags = flags; }
    void SetDoHTML              (bool val);
    void SetHideImpFeats        (bool val);
    void SetHideSNPFeatures     (bool val);
    void SetHideExonFeatures    (bool val);
    void SetHideIntronFeatures  (bool val);
    void SetHideRemoteImpFeats  (bool val);
    void SetHideGeneRIFs        (bool val);
    void SetOnlyGeneRIFs        (bool val);
    void SetHideCDSProdFeatures (bool val);
    void SetHideCDDFeats        (bool val);
    void SetLatestGeneRIFs      (bool val);
    void SetShowContigFeatures  (bool val);
    void SetShowContigSources   (bool val);
    void SetShowContigAndSeq    (bool val);
    void SetCopyGeneToCDNA      (bool val);
    void SetCopyCDSFromCDNA     (bool val);
    void SetHideSourceFeats     (bool val);
    void SetAlwaysTranslateCDS  (bool val);
    void SetShowFarTranslations (bool val);
    void SetTranslateIfNoProduct(bool val);
    void SetShowTranscript      (bool val);
    void SetShowPeptides        (bool val);
    void SetShowFtableRefs      (bool val);
    void SetOldFeatsOrder       (bool val);
    void SetHtml                (bool val);

private:
    
    static const bool sm_ModeFlags[4][26];

    // data
    TFormat     m_Format;
    TMode       m_Mode;
    TStyle      m_Style;
    TView       m_View;
    TFlags      m_Flags;
};


/////////////////////////////////////////////////////////////////////////////
// inilne methods

// custom flags
#define CUSTOM_FLAG_GET(x) inline \
bool CFlatFileConfig::x(void) const \
{ \
    return (m_Flags & f##x) != 0; \
}

#define CUSTOM_FLAG_SET(x) inline \
void CFlatFileConfig::Set##x(bool val) \
{ \
    if ( val ) { \
        m_Flags |= f##x; \
    } else { \
        m_Flags &= ~f##x; \
    } \
}

#define CUSTOM_FLAG_IMP(x) \
CUSTOM_FLAG_GET(x) \
CUSTOM_FLAG_SET(x)

CUSTOM_FLAG_IMP(DoHTML)
CUSTOM_FLAG_IMP(HideImpFeats)
CUSTOM_FLAG_IMP(HideSNPFeatures)
CUSTOM_FLAG_IMP(HideExonFeatures)
CUSTOM_FLAG_IMP(HideIntronFeatures)
CUSTOM_FLAG_IMP(HideRemoteImpFeats)
CUSTOM_FLAG_IMP(HideGeneRIFs)
CUSTOM_FLAG_IMP(OnlyGeneRIFs)
CUSTOM_FLAG_IMP(HideCDSProdFeatures)
CUSTOM_FLAG_IMP(HideCDDFeats)
CUSTOM_FLAG_IMP(LatestGeneRIFs)
CUSTOM_FLAG_IMP(ShowContigFeatures)
CUSTOM_FLAG_IMP(ShowContigSources)
CUSTOM_FLAG_IMP(ShowContigAndSeq)
CUSTOM_FLAG_IMP(CopyGeneToCDNA)
CUSTOM_FLAG_IMP(CopyCDSFromCDNA)
CUSTOM_FLAG_IMP(HideSourceFeats)
CUSTOM_FLAG_IMP(AlwaysTranslateCDS)
CUSTOM_FLAG_IMP(ShowFarTranslations)
CUSTOM_FLAG_IMP(TranslateIfNoProduct)
CUSTOM_FLAG_IMP(ShowTranscript)
CUSTOM_FLAG_IMP(ShowPeptides)
CUSTOM_FLAG_IMP(ShowFtableRefs)
CUSTOM_FLAG_IMP(OldFeatsOrder)

#undef CUSTOM_FLAG_IMP
#undef CUSTOM_FLAG_GET
#undef CUSTOM_FLAG_SET

// end of inline methods
/////////////////////////////////////////////////////////////////////////////

END_SCOPE(objects)
END_NCBI_SCOPE


/*
* ===========================================================================
*
* $Log: flat_file_config.hpp,v $
* Revision 1000.0  2004/06/01 19:48:19  gouriano
* PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.2
*
* Revision 1.2  2004/04/23 14:13:48  gorelenk
* Added missed export prefix to declaration of class CFlatFileConfig.
*
* Revision 1.1  2004/04/22 15:48:36  shomrat
* Initial Revision (adapted from context.hpp)
*
*
* ===========================================================================
*/


#endif  /* OBJTOOLS_FORMAT___FLAT_FILE_CONFIG__HPP */