locus_item.cpp

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         (ctx.IsDelta()  &&  !ctx.IsDeltaLitOnly()) ) {
        m_Division = "CON";
        return;
    }

    const CBioseq_Handle& bsh = ctx.GetHandle();
    const CBioSource* bsrc = 0;

    // Find the BioSource object for this sequnece.
    CSeqdesc_CI src_desc(bsh, CSeqdesc::e_Source);
    if ( src_desc ) {
        bsrc = &(src_desc->GetSource());
    } else {
        CFeat_CI feat(bsh, 0, 0, CSeqFeatData::e_Biosrc);
        if ( feat ) {
            bsrc = &(feat->GetData().GetBiosrc());
        } else if ( ctx.IsProt() ) {
            // if protein with no sources, get sources applicable to 
            // DNA location of CDS
            const CSeq_feat* cds = GetCDSForProduct(bsh);
            if ( cds ) {
                CConstRef<CSeq_feat> nuc_fsrc = GetBestOverlappingFeat(
                    cds->GetLocation(),
                    CSeqFeatData::e_Biosrc,
                    eOverlap_Contains,
                    bsh.GetScope());
                if ( nuc_fsrc ) {
                    bsrc = &(nuc_fsrc->GetData().GetBiosrc());
                } else {
                    CBioseq_Handle nuc = 
                        bsh.GetScope().GetBioseqHandle(cds->GetLocation());
                    CSeqdesc_CI nuc_dsrc(nuc, CSeqdesc::e_Source);
                    if ( nuc_dsrc ) {
                        bsrc = &(nuc_dsrc->GetSource());
                    }
                }
            }
        }
    }

    bool is_transgenic = false;

    if ( bsrc ) {
        CBioSource::TOrigin origin = bsrc->GetOrigin();
        if ( bsrc->CanGetOrg() ) {
            const COrg_ref& org = bsrc->GetOrg();
            if ( org.CanGetOrgname()  &&  org.GetOrgname().CanGetDiv() ) {
                m_Division = org.GetOrgname().GetDiv();
            }
        }

        ITERATE(CBioSource::TSubtype, subsource, bsrc->GetSubtype() ) {
            if ( (*subsource)->CanGetSubtype()  &&
                (*subsource)->GetSubtype() == CSubSource::eSubtype_transgenic ) {
                is_transgenic = true;
            }
        }
        
        switch ( ctx.GetTech() ) {
        case CMolInfo::eTech_est:
            m_Division = "EST";
            break;
        case CMolInfo::eTech_sts:
            m_Division = "STS";
            break;
        case CMolInfo::eTech_survey:
            m_Division = "GSS";
            break;
        case CMolInfo::eTech_htgs_0:
        case CMolInfo::eTech_htgs_1:
        case CMolInfo::eTech_htgs_2:
            m_Division = "HTG";
            break;
        case CMolInfo::eTech_htc:
            m_Division = "HTC";
            break;
        default:
            break;
        }

        if ( origin == CBioSource::eOrigin_synthetic  ||  is_transgenic ) {
            m_Division = "SYN";
        }

        ITERATE( CBioseq::TId, id, bsh.GetBioseqCore()->GetId() ) {
            if ( (*id)->IdentifyAccession() == CSeq_id::eAcc_patent ) {
                m_Division = "PAT";
                break;
            }
        }

        // more complicated code for division, if necessary, goes here
        
        for ( CSeqdesc_CI gb_desc(bsh, CSeqdesc::e_Genbank); gb_desc; ++gb_desc ) {
            const CGB_block& gb = gb_desc->GetGenbank();
            if ( gb.CanGetDiv() ) {
                if ( m_Division.empty()    ||
                     gb.GetDiv() == "SYN"  ||
                     gb.GetDiv() == "PAT" ) {
                    m_Division = gb.GetDiv();
                }
            }
        }

        const CMolInfo* molinfo = dynamic_cast<const CMolInfo*>(GetObject());
        if ( ctx.Config().IsFormatEMBL() ) {
            for ( CSeqdesc_CI embl_desc(bsh, CSeqdesc::e_Embl); 
                  embl_desc; 
                  ++embl_desc ) {
                const CEMBL_block& embl = embl_desc->GetEmbl();
                if ( embl.CanGetDiv() ) {
                    if ( embl.GetDiv() == CEMBL_block::eDiv_other  &&
                         molinfo == 0 ) {
                        m_Division = "HUM";
                    } else {
                        m_Division = embl.GetDiv();
                    }
                }
            }
        }
    }

    // Set a default value (3 spaces)
    if ( m_Division.empty() ) {
        m_Division = "   ";
    }
}


// Date

void CLocusItem::x_SetDate(CBioseqContext& ctx)
{
    const CBioseq_Handle& bsh = ctx.GetHandle();

    const CDate* date = x_GetDateForBioseq(bsh);
    if ( date == 0 ) {
        // if bioseq is product of CDS or mRNA feature, get 
        // date from parent bioseq.
        CBioseq_Handle parent = GetNucleotideParent(bsh);
        if ( parent ) {
            date = x_GetDateForBioseq(parent);
        }
    }

    if ( date ) {
        m_Date.erase();
        DateToString(*date, m_Date);
    }
}


const CDate* CLocusItem::x_GetDateForBioseq(const CBioseq_Handle& bsh) const
{
    const CDate* result = 0;

    {{
        CSeqdesc_CI desc(bsh, CSeqdesc::e_Update_date);
        if ( desc ) {
            result = &(desc->GetUpdate_date());
        }
    }}

    {{
        // temporarily (???) also look at genbank block entry date 
        CSeqdesc_CI desc(bsh, CSeqdesc::e_Genbank);
        if ( desc ) {
            const CGB_block& gb = desc->GetGenbank();
            if ( gb.CanGetEntry_date() ) {
                result = x_GetLaterDate(result, &gb.GetEntry_date());
            }
        }
    }}

    {{
        CSeqdesc_CI desc(bsh, CSeqdesc::e_Embl);
        if ( desc ) {
            const CEMBL_block& embl = desc->GetEmbl();
            if ( embl.CanGetCreation_date() ) {
                result = x_GetLaterDate(result, &embl.GetCreation_date());
            }
            if ( embl.CanGetUpdate_date() ) {
                result = x_GetLaterDate(result, &embl.GetUpdate_date());
            }
        }
    }}

    {{
        CSeqdesc_CI desc(bsh, CSeqdesc::e_Sp);
        if ( desc ) {
            const CSP_block& sp = desc->GetSp();
            if ( sp.CanGetCreated()  &&  sp.GetCreated().IsStd() ) {
                result = x_GetLaterDate(result, &sp.GetCreated());
            }
            if ( sp.CanGetSequpd()  &&  sp.GetSequpd().IsStd() ) {
                result = x_GetLaterDate(result, &sp.GetSequpd());
            }
            if ( sp.CanGetAnnotupd()  &&  sp.GetAnnotupd().IsStd() ) {
                result = x_GetLaterDate(result, &sp.GetAnnotupd());
            }
        }
    }}

    {{
        CSeqdesc_CI desc(bsh, CSeqdesc::e_Pdb);
        if ( desc ) {
            const CPDB_block& pdb = desc->GetPdb();
            if ( pdb.CanGetDeposition()  &&  pdb.GetDeposition().IsStd() ) {
                result = x_GetLaterDate(result, &pdb.GetDeposition());
            }
            if ( pdb.CanGetReplace() ) {
                const CPDB_replace& replace = pdb.GetReplace();
                if ( replace.CanGetDate()  &&   replace.GetDate().IsStd() ) {
                    result = x_GetLaterDate(result, &replace.GetDate());
                }
            }
        }
    }}

    {{
        CSeqdesc_CI desc(bsh, CSeqdesc::e_Create_date);
        if ( desc ) {
            result = x_GetLaterDate(result, &(desc->GetCreate_date()));
        }
    }}

    return result;
}


const CDate* CLocusItem::x_GetLaterDate(const CDate* d1, const CDate* d2) const
{
    if ( d1 == 0 ) {
        return d2;
    }

    if ( d2 == 0 ) {
        return d1;
    }

    return (d1->Compare(*d2) == CDate::eCompare_after) ? d1 : d2;
}


END_SCOPE(objects)
END_NCBI_SCOPE


/*
* ===========================================================================
*
* $Log: locus_item.cpp,v $
* Revision 1000.2  2004/06/01 19:45:04  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.9
*
* Revision 1.9  2004/05/21 21:42:54  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.8  2004/04/22 15:58:51  shomrat
* Changes in context
*
* Revision 1.7  2004/04/13 16:49:01  shomrat
* GBSeq format changes
*
* Revision 1.6  2004/03/25 20:45:05  shomrat
* Use handles
*
* Revision 1.5  2004/03/05 18:41:14  shomrat
* bug fix
*
* Revision 1.4  2004/02/13 14:23:08  shomrat
* force CON division for contig style and genome view
*
* Revision 1.3  2004/02/11 22:55:12  shomrat
* use IsFormatEMBL method
*
* Revision 1.2  2003/12/18 17:43:35  shomrat
* context.hpp moved
*
* Revision 1.1  2003/12/17 20:23:35  shomrat
* Initial Revision (adapted from flat lib)
*
*
* ===========================================================================
*/