context.cpp

来自「ncbi源码」· C++ 代码 · 共 601 行 · 第 1/2 页

                (len == 13  &&  NStr::EndsWith(acc, "0000000"));
            if ( m_IsWGSMaster ) {
                m_WGSMasterAccn = acc;
                m_WGSMasterName = tsip->CanGetName() ? tsip->GetName() : kEmptyStr;
            }
        } 

        // GBB source
        m_ShowGBBSource = m_ShowGBBSource  ||  
                          ((acc_type & CSeq_id::eAcc_gsdb_dirsub) != 0);
    }
}


CSeq_inst::TRepr CBioseqContext::x_GetRepr(void) const
{
    return m_Handle.IsSetInst_Repr() ?
        m_Handle.GetInst_Repr() : CSeq_inst::eRepr_not_set;
}


const CMolInfo* CBioseqContext::x_GetMolInfo(void) const
{
    CSeqdesc_CI desc(m_Handle, CSeqdesc::e_Molinfo);
    return desc ? &desc->GetMolinfo() : 0;
}


bool CBioseqContext::x_IsPart() const
{
    if ( m_Repr == CSeq_inst::eRepr_raw    ||
         m_Repr == CSeq_inst::eRepr_const  ||
         m_Repr == CSeq_inst::eRepr_delta  ||
         m_Repr == CSeq_inst::eRepr_virtual ) {
        CSeq_entry_Handle eh = m_Handle.GetParentEntry();
        _ASSERT(eh  &&  eh.IsSeq());

        eh = eh.GetParentEntry();
        if ( eh  &&  eh.IsSet() ) {
            CBioseq_set_Handle bsst = eh.GetSet();
            if ( bsst.IsSetClass()  &&  
                 bsst.GetClass() == CBioseq_set::eClass_parts ) {
                return true;
            }
        }
    }
    return false;
}


bool CBioseqContext::x_HasParts(void) const
{
    _ASSERT(IsSegmented());

    CSeq_entry_Handle h =
        m_Handle.GetExactComplexityLevel(CBioseq_set::eClass_segset);
    if ( !h ) {
        return false;
    }
    
    // make sure the segmented set contains our bioseq
    {{
        bool has_seq = false;
        for ( CSeq_entry_CI it(h); it; ++it ) {
            if ( it->IsSeq()  &&  it->GetSeq() == m_Handle ) {
                has_seq = true;
                break;
            }
        }
        if ( !has_seq ) {
            return false;
        }
    }}

    // find the parts set
    {{
        for ( CSeq_entry_CI it(h); it; ++it ) {
            if ( it->IsSet()  &&  it->GetSet().IsSetClass()  &&
                it->GetSet().GetClass() == CBioseq_set::eClass_parts ) {
                return true;
            }
        }
    }}

    return false;
}


bool CBioseqContext::x_IsDeltaLitOnly(void) const
{
    _ASSERT(IsDelta());

    if ( m_Handle.IsSetInst_Ext() ) {
        const CBioseq_Handle::TInst_Ext& ext = m_Handle.GetInst_Ext();
        if ( ext.IsDelta() ) {
            ITERATE (CDelta_ext::Tdata, it, ext.GetDelta().Get()) {
                if ( (*it)->IsLoc() ) {
                    return false;
                }
            }
        }
    }
    return true;
}


SIZE_TYPE CBioseqContext::x_GetPartNumber(void)
{
    return m_Master ? m_Master->GetPartNumber(m_Handle) : 0;
}


bool CBioseqContext::x_IsInGPS(void) const
{
    CSeq_entry_Handle e = 
        m_Handle.GetExactComplexityLevel(CBioseq_set::eClass_gen_prod_set);
    return e;
}


bool CBioseqContext::x_IsInNucProt(void) const
{
    CSeq_entry_Handle e = 
        m_Handle.GetExactComplexityLevel(CBioseq_set::eClass_nuc_prot);
    return e;
}


bool CBioseqContext::DoContigStyle(void) const
{
    const CFlatFileConfig& cfg = Config();
    if ( cfg.IsStyleContig() ) {
        return true;
    } else if ( cfg.IsStyleNormal() ) {
        if ( (IsSegmented()  &&  !HasParts())  ||
             (IsDelta()  &&  !IsDeltaLitOnly()) ) {
            return true;
        }
    }

    return false;
}


/////////////////////////////////////////////////////////////////////////////
//
// CMasterContext


CMasterContext::CMasterContext(const CBioseq_Handle& seq) :
    m_Handle(seq)
{
    _ASSERT(seq);
    _ASSERT(seq.GetInst_Ext().IsSeg());

    x_SetNumParts();
    x_SetBaseName();
}


CMasterContext::~CMasterContext(void)
{
}


SIZE_TYPE CMasterContext::GetPartNumber(const CBioseq_Handle& part)
{
    if ( !part ) {
        return 0;
    }
    CScope& scope = m_Handle.GetScope();

    SIZE_TYPE serial = 1;
    ITERATE (CSeg_ext::Tdata, it, m_Handle.GetInst_Ext().GetSeg().Get()) {
        if ( (*it)->IsNull() ) {
            continue;
        }
        const CSeq_id& id = GetId(**it);
        CBioseq_Handle bsh = scope.GetBioseqHandleFromTSE(id, m_Handle);
        if ( bsh   &&  bsh == part ) {
            return serial;
        }
        ++serial;
    }

    return 0;
}


void CMasterContext::x_SetNumParts(void)
{
    SIZE_TYPE count = 0;
    // count only non-gap parts
    ITERATE (CSeg_ext::Tdata, it, m_Handle.GetInst_Ext().GetSeg().Get()) {
        if ( (*it)->IsNull() ) {
            continue;
        }
        ++count;
    }
    m_NumParts = count;
}


void CMasterContext::x_SetBaseName(void)
{
    // !!!
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ===========================================================================
*
* $Log: context.cpp,v $
* Revision 1000.1  2004/06/01 19:43:52  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.18
*
* Revision 1.18  2004/05/21 21:42:54  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.17  2004/05/08 12:11:39  dicuccio
* Use CSeq_id::GetLabel() instead of GetSeqIdString()
*
* Revision 1.16  2004/05/06 17:48:49  shomrat
* + IsEMBL and IsInNucProt
*
* Revision 1.15  2004/04/27 15:12:24  shomrat
* Added logic for partial range formatting
*
* Revision 1.14  2004/04/22 15:52:00  shomrat
* Refactring of context
*
* Revision 1.13  2004/03/31 17:15:09  shomrat
* name changes
*
* Revision 1.12  2004/03/26 17:23:38  shomrat
* fixed initialization of m_IsWGS
*
* Revision 1.11  2004/03/25 20:36:02  shomrat
* Use handles
*
* Revision 1.10  2004/03/24 18:57:04  vasilche
* CBioseq_Handle::GetComplexityLevel() now returns CSeq_entry_Handle.
*
* Revision 1.9  2004/03/18 15:36:26  shomrat
* + new flag ShowFtableRefs
*
* Revision 1.8  2004/03/10 21:25:42  shomrat
* Fix m_RefseqInfo initialization
*
* Revision 1.7  2004/03/05 18:46:26  shomrat
* Added customization flags
*
* Revision 1.6  2004/02/19 18:03:29  shomrat
* changed implementation of GetPreferredSynonym
*
* Revision 1.5  2004/02/11 22:49:04  shomrat
* using types in flag file
*
* Revision 1.4  2004/02/11 16:49:16  shomrat
* added user customization flags
*
* Revision 1.3  2004/01/14 16:09:04  shomrat
* multiple changes (work in progress)
*
* Revision 1.2  2003/12/18 17:43:31  shomrat
* context.hpp moved
*
* Revision 1.1  2003/12/17 20:18:44  shomrat
* Initial Revision (adapted from flat lib)
*
* Revision 1.4  2003/06/02 16:06:42  dicuccio
* Rearranged src/objects/ subtree.  This includes the following shifts:
*     - src/objects/asn2asn --> arc/app/asn2asn
*     - src/objects/testmedline --> src/objects/ncbimime/test
*     - src/objects/objmgr --> src/objmgr
*     - src/objects/util --> src/objmgr/util
*     - src/objects/alnmgr --> src/objtools/alnmgr
*     - src/objects/flat --> src/objtools/flat
*     - src/objects/validator --> src/objtools/validator
*     - src/objects/cddalignview --> src/objtools/cddalignview
* In addition, libseq now includes six of the objects/seq... libs, and libmmdb
* replaces the three libmmdb? libs.
*
* Revision 1.3  2003/03/21 18:49:17  ucko
* Turn most structs into (accessor-requiring) classes; replace some
* formerly copied fields with pointers to the original data.
*
* Revision 1.2  2003/03/11 15:37:51  kuznets
* iterate -> ITERATE
*
* Revision 1.1  2003/03/10 16:39:09  ucko
* Initial check-in of new flat-file generator
*
*
* ===========================================================================
*/