NCBI C++ Toolkit Cross Reference

/*  $Id: snp_bitfield_factory.cpp 75466 2016-11-17 23:39:13Z rudnev $
 * ===========================================================================
 *
 *                            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:  Melvin Quintos
 *
 * File Description:
 *  Provides implementation of CSnpBitfieldFactoryclass.
 *   See snp_bitfield_factory.hpp for class usage.
 *
 */

#include <ncbi_pch.hpp>

#include "snp_bitfield_factory.hpp"
#include "snp_bitfield_1_2.hpp"
#include "snp_bitfield_2.hpp"
#include "snp_bitfield_3.hpp"
#include "snp_bitfield_4.hpp"
#include "snp_bitfield_5.hpp"
#include "snp_bitfield_20.hpp"

#include <objects/general/User_field.hpp>
#include <objects/general/User_object.hpp>

BEGIN_NCBI_SCOPE
USING_SCOPE(objects);

///////////////////////////////////////////////////////////////////////////////
//  Public Methods
///////////////////////////////////////////////////////////////////////////////
CSnpBitfield::IEncoding *
CSnpBitfieldFactory::CreateBitfield(const CSeq_feat& feat)
{
    CSnpBitfield::IEncoding *bitfield = 0;
    // LOG_POST(Error << "Processing feature:");
    // LOG_POST(Error << MSerial_AsnText << feat);

    if(feat.IsSetExt()) {
        const CUser_object& user(feat.GetExt());
        // first try "Bitfield", that's where SNP 2.0 bitfields are stored
        {
            CConstRef<CUser_field> field(user.GetFieldRef("Bitfield"));
            if(field && field->CanGetData() && field->GetData().IsOs()) {
                const vector<char>& data(field->GetData().GetOs());

                // check size
                size_t size(data.size());

                // VDB based SNP 2.0 bitfield has 96 bits (8 bytes)
                // it also uses some info from the feature itself, so is initialized from the feature, not the byte sequence
                if (size == 8) {
                    bitfield = new CSnpBitfield20(feat);
                }
            }
        }
        // if a bitfield was not found, try legacy storage scheme in "QualityCodes"
        if(!bitfield) {
            CConstRef<CUser_field> field(user.GetFieldRef("QualityCodes"));
            if(field && field->CanGetData() && field->GetData().IsOs()) {
                const vector<char>& data(field->GetData().GetOs());

                // check size
                size_t size(data.size());

                // Only v1.2 and on are supported.  Previous versions were incorrectly
                //   encoded

                // For 1.2 version, there exists 10 bytes
                if (size == 10) {
                    bitfield = new CSnpBitfield1_2(feat);
                }
                // other supported versions before VDB based SNP 2.0 have 12 bytes (96 bits) and
                // maintain a version number in least significant byte
                else if (size == 12) {
                    unsigned char version = (unsigned char)data[0];
                    switch(version) {
                        case 2:     bitfield = new CSnpBitfield2(feat);     break;
                        case 3:     bitfield = new CSnpBitfield3(feat);     break;
                        case 4:     bitfield = new CSnpBitfield4(feat);     break;
                        case 5:     bitfield = new CSnpBitfield5(feat);     break;

                        // if version was undetected,
                        //   use last known version
                        default:
                            bitfield = new CSnpBitfield5(feat);
                            break;
                    }
                }
            }
        }
    }

    // if no bitfield created, create a null bitfield
    if (bitfield == 0) {
        bitfield = new CSnpBitfieldNull();
    }

    return bitfield;
}


///////////////////////////////////////////////////////////////////////////////
//  CSnpBitfieldNull - the Null Object of CSnpBitfield::IEncoding
///////////////////////////////////////////////////////////////////////////////
bool CSnpBitfieldNull::IsTrue( CSnpBitfield::EProperty e ) const
{
    return false;
}

bool CSnpBitfieldNull::IsTrue( CSnpBitfield::EFunctionClass e ) const
{
    return false;
}

int  CSnpBitfieldNull::GetWeight() const
{
    return 0;
}

int  CSnpBitfieldNull::GetVersion() const
{
    return 0;
}

CSnpBitfield::IEncoding * CSnpBitfieldNull::Clone()
{
    return new CSnpBitfieldNull();
}

CSnpBitfield::EFunctionClass CSnpBitfieldNull::GetFunctionClass() const
{
    return CSnpBitfield::eUnknownFxn;
}

CSnpBitfield::EVariationClass CSnpBitfieldNull::GetVariationClass() const
{
    return CSnpBitfield::eUnknownVariation;
}


END_NCBI_SCOPE