context.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: context.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 19:43:52  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.18
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: context.cpp,v 1000.1 2004/06/01 19:43:52 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.
*
* ===========================================================================
*
* Author:  Aaron Ucko, NCBI
*          Mati Shomrat
*
* File Description:
*   new (early 2003) flat-file generator -- context needed when (pre)formatting
*
* ===========================================================================
*/
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>

#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seq/Seg_ext.hpp>
#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Delta_seq.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seqloc/Textseq_id.hpp>
#include <objects/general/Dbtag.hpp>

#include <objmgr/scope.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/seq_entry_handle.hpp>
#include <objmgr/seq_entry_ci.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/seq_loc_mapper.hpp>

#include <objtools/format/context.hpp>


BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
USING_SCOPE(sequence);


/////////////////////////////////////////////////////////////////////////////
//
// CBioseqContext

// constructor
CBioseqContext::CBioseqContext
(const CBioseq_Handle& seq,
 CFlatFileContext& ffctx,
 CMasterContext* mctx) :
    m_Handle(seq),
    m_Repr(CSeq_inst::eRepr_not_set),
    m_Mol(CSeq_inst::eMol_not_set),
    m_HasParts(false),
    m_IsPart(false),
    m_PartNumber(0),
    m_IsDeltaLitOnly(false),
    m_IsProt(false),
    m_IsInGPS(false),
    m_IsInNucProt(false),
    m_IsGED(false),
    m_IsEMBL(false),
    m_IsPDB(false),
    m_IsSP(false),
    m_IsTPA(false),
    m_IsRefSeq(false),
    m_RefseqInfo(0),
    m_IsGbGenomeProject(false),  // GenBank Genome project data (AE)
    m_IsNcbiCONDiv(false),       // NCBI CON division (CH)
    m_IsPatent(false),
    m_IsGI(false),
    m_IsWGS(false),
    m_IsWGSMaster(false),
    m_IsHup(false),
    m_Gi(0),
    m_ShowGBBSource(false),
    m_FFCtx(ffctx),
    m_Master(mctx)
{
    x_Init(seq, m_FFCtx.GetLocation());
}


// destructor
CBioseqContext::~CBioseqContext(void)
{
}


const CSeq_id& CBioseqContext::GetPreferredSynonym(const CSeq_id& id) const
{
    if ( id.IsGi()  &&  id.GetGi() == m_Gi ) {
        return *m_PrimaryId;
    }

    CBioseq_Handle h = m_Handle.GetScope().GetBioseqHandleFromTSE(id, m_Handle);
    if ( h ) {
        if ( h == m_Handle ) {
            return *m_PrimaryId;
        } else if ( h.GetSeqId().NotEmpty() ) {
            return *FindBestChoice(h.GetBioseqCore()->GetId(), CSeq_id::Score);
        }
    }

    return id;
}



// initialization
void CBioseqContext::x_Init(const CBioseq_Handle& seq, const CSeq_loc* user_loc)
{
    _ASSERT(seq);
    _ASSERT(seq.IsSetInst());

    // NB: order of execution is important
    x_SetId();
    m_Repr = x_GetRepr();
    m_Mol  = seq.GetInst_Mol();
    m_Molinfo.Reset(x_GetMolInfo());

    if ( IsSegmented() ) {
        m_HasParts = x_HasParts();
    }
    m_IsPart = x_IsPart();
    if ( m_IsPart ) {
        _ASSERT(m_Master);
        m_PartNumber = x_GetPartNumber();
    }
    if ( IsDelta() ) {
        m_IsDeltaLitOnly = x_IsDeltaLitOnly();
    }

    m_IsProt = CSeq_inst::IsAa(seq.GetInst_Mol());

    m_IsInGPS     = x_IsInGPS();
    m_IsInNucProt = x_IsInNucProt();

    x_SetLocation(user_loc);
    
}


void CBioseqContext::x_SetLocation(const CSeq_loc* user_loc)
{
    _ASSERT(user_loc == 0  ||  user_loc->IsInt()  ||  user_loc->IsWhole());
    CRef<CSeq_loc> source;

    if ( user_loc != 0 ) {
        // map the location to the current bioseq
        CSeq_loc_Mapper mapper(m_Handle);
        mapper.SetMergeAll();  // just to be safe
        source.Reset(mapper.Map(*user_loc));
        
        // no need to map if doing the entire bioseq
        if ( source->IsWhole()  ||
             source->GetStart(kInvalidSeqPos) == 0  &&
             source->GetEnd(kInvalidSeqPos) == m_Handle.GetInst_Length() - 1) {
            source.Reset();
        }
        _ASSERT(!source  ||  source->IsInt());

        if ( source ) {
            CScope& scope = GetScope();

            CSeq_loc target;
            target.SetInt().SetFrom(0);
            target.SetInt().SetTo(GetLength(*source, &scope) - 1);
            target.SetId(*m_PrimaryId);

            m_Mapper.Reset(new CSeq_loc_Mapper(*source, target, &scope));
            m_Mapper->SetMergeAbutting();
            m_Mapper->PreserveDestinationLocs();  // ???
            m_Mapper->KeepNonmappingRanges();
        }
    }
    // if no location is specified do the entire sequence
    if ( !source ) {
        source.Reset(new CSeq_loc);
        source->SetWhole(*m_PrimaryId);
    }
    _ASSERT(source);
    m_Location = source;

    
}


void CBioseqContext::x_SetId(void)
{
    m_PrimaryId.Reset(new CSeq_id);
    m_PrimaryId->Assign(sequence::GetId(m_Handle, sequence::eGetId_Best));

    m_Accession.erase();
    m_PrimaryId->GetLabel(&m_Accession, CSeq_id::eContent);

    ITERATE (CBioseq::TId, id_iter, m_Handle.GetBioseqCore()->GetId()) {
        const CSeq_id& id = **id_iter;
        const CTextseq_id* tsip = id.GetTextseq_Id();
        const string& acc = (tsip != 0  &&  tsip->CanGetAccession()) ?
            tsip->GetAccession() : kEmptyStr;

        CSeq_id::EAccessionInfo acc_info = id.IdentifyAccession();
        unsigned int acc_type = acc_info & CSeq_id::eAcc_type_mask;
        unsigned int acc_div =  acc_info & CSeq_id::eAcc_division_mask;

        switch ( id.Which() ) {
        // Genbank, Embl or Ddbj
        case CSeq_id::e_Embl:
            m_IsEMBL = true;
            // intentional fall through
        case CSeq_id::e_Genbank:
        case CSeq_id::e_Ddbj:
            m_IsGED = true;
            m_IsGbGenomeProject = m_IsGbGenomeProject  ||
                ((acc_type & CSeq_id::eAcc_gb_genome) != 0);
            m_IsNcbiCONDiv = m_IsNcbiCONDiv  ||
                ((acc_type & CSeq_id::eAcc_gb_con) != 0);
            break;
        // Patent
        case CSeq_id::e_Patent:
            m_IsPatent = true;
            break;
        // RefSeq
        case CSeq_id::e_Other:
            m_IsRefSeq = true;
            m_RefseqInfo = acc_info;
            break;
        // Gi
        case CSeq_id::e_Gi:
            m_IsGI = true;
            m_Gi = id.GetGi();
            break;
        // PDB
        case CSeq_id::e_Pdb:
            m_IsPDB = true;
            break;
        // TPA
        case CSeq_id::e_Tpg:
        case CSeq_id::e_Tpe:
        case CSeq_id::e_Tpd:
            m_IsTPA = true;
            break;
        case CSeq_id::e_General:
            if ( id.GetGeneral().CanGetDb() ) {
                if ( !NStr::CompareCase(id.GetGeneral().GetDb(), "BankIt") ) {
                    m_IsTPA = true;
                }
            }
            break;
        // nothing special
        case CSeq_id::e_not_set:
        case CSeq_id::e_Local:
        case CSeq_id::e_Gibbsq:
        case CSeq_id::e_Gibbmt:
        case CSeq_id::e_Giim:
        case CSeq_id::e_Pir:
        case CSeq_id::e_Swissprot:
            m_IsSP = true;
            break;
        case CSeq_id::e_Prf:
        default:
            break;
        }

        // WGS
        m_IsWGS = m_IsWGS  ||  (acc_div == CSeq_id::eAcc_wgs);
        
        if ( m_IsWGS  &&  !acc.empty() ) {
            size_t len = acc.length();
            m_IsWGSMaster = 
                ((len == 12  ||  len == 15)  &&  NStr::EndsWith(acc, "000000"))  ||