text_object_description.cpp

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/*  $Id: text_object_description.cpp 94996 2021-09-27 14:11:38Z grichenk $
* ===========================================================================
*
*                            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: Sema Kachalo
*
* File Description:
*   Getting text description for CSeq_feat / CSeqdesc / CBioseq / CBioseq_set objects
*/
 
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <objects/general/Date.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/User_object.hpp>
#include <objects/pub/Pub_equiv.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seqloc/Seq_bond.hpp>
#include <objects/seqloc/Seq_loc_equiv.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/edit/text_object_description.hpp>
 
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
BEGIN_SCOPE(edit)
 
static bool IsAccession(const CSeq_id& id)
{
    return id.Which() == CSeq_id::e_Genbank
        || id.Which() == CSeq_id::e_Ddbj
        || id.Which() == CSeq_id::e_Embl
        || id.Which() == CSeq_id::e_Other;
}
 
 
static CConstRef<CSeq_id> GetBestId(const CBioseq& bioseq)
{
    const CBioseq::TId& seq_id_ls = bioseq.GetId();
    CConstRef<CSeq_id> best_seq_id;
    int best_score = CSeq_id::kMaxScore;
    for (auto it: seq_id_ls) {
        if (IsAccession(*it)) {
            return it;
        }
        else {
            int score = it->BaseBestRankScore();
            if (best_score > score) {
                best_seq_id = it;
                best_score = score;
            }
        }
    }
    return best_seq_id;
}
 
 
static string GetTextObjectDescription(CBioseq_set_Handle bssh)
{
    CNcbiOstrstream result_strm;
 
    CBioseq_set::EClass bioseq_set_class = bssh.IsSetClass() ? bssh.GetClass() : CBioseq_set::eClass_not_set;
    if (bioseq_set_class == CBioseq_set::eClass_segset || bioseq_set_class == CBioseq_set::eClass_nuc_prot) {
        switch (bioseq_set_class) {
            case CBioseq_set::eClass_segset:
                result_strm << "ss|";
                break;
            case CBioseq_set::eClass_nuc_prot:
                result_strm << "np|";
                break;
            default:
                _TROUBLE;
        }
 
        // get representative bioseq from bioseq-set
        CBioseq_CI bioseq_ci(bssh);
        if (!bioseq_ci) {
            return "(EMPTY BIOSEQ-SET)";
        }
        const CBioseq_Handle & main_bsh = *bioseq_ci;
        CConstRef<CSeq_id> best_seq_id = GetBestId(*main_bsh.GetCompleteBioseq());
        _ASSERT(best_seq_id);  // a Bioseq must have at least one Seq-id
        {
            string seq_id_str;
            best_seq_id->GetLabel(&seq_id_str, CSeq_id::eContent);
            result_strm << seq_id_str;
        }
 
    }
    else {
        // get first child of bssh (which could be a bioseq or bioseq-set)
        CSeq_entry_CI direct_child_ci(bssh); // NOT recursive
        if (!direct_child_ci) {
            // no child, so this is the best we can do
            return "BioseqSet";
        }
 
        result_strm << "Set containing ";
        if (direct_child_ci->IsSeq()) {
            CConstRef<CSeq_id> best_seq_id = GetBestId(*direct_child_ci->GetSeq().GetCompleteBioseq());
            _ASSERT(best_seq_id);  // a Bioseq must have at least one Seq-id
            {
                string seq_id_str;
                best_seq_id->GetLabel(&seq_id_str, CSeq_id::eContent);
                result_strm << seq_id_str;
            }
        }
        else {
            _ASSERT(direct_child_ci->IsSet());
            result_strm << GetTextObjectDescription(direct_child_ci->GetSet());
        }
    }
 
    return CNcbiOstrstreamToString(result_strm);
}
 
 
static void GetSeqFeatLabel(const CSeq_feat& seq_feat, string& label)
{
    label = kEmptyStr;
 
    feature::GetLabel(seq_feat, &label, feature::fFGL_Content);
    size_t pos;
    if (seq_feat.GetData().IsRna() && !label.empty() && (string::npos != (pos = label.find("RNA-")))) {
        label = label.substr(pos + 4);
    }
    string number = "/number=";
    if (!label.empty()
        && (seq_feat.GetData().GetSubtype() == CSeqFeatData::eSubtype_exon
            || seq_feat.GetData().GetSubtype()
            == CSeqFeatData::eSubtype_intron)
        && (string::npos != (pos = label.find(number)))) {
        label = label.substr(pos + number.size());
        if (label.find("exon") == 0 || label.find("intron") == 0) { // pos
            label = label.substr(0, label.find(' '));
        }
    }
}
 
 
static void UpgradeSeqLocId(CSeq_point& pnt, CScope& scope)
{
    if (pnt.IsSetId()) {
        CBioseq_Handle bsh = scope.GetBioseqHandle(pnt.GetId());
        if (bsh) {
            CConstRef<CSeq_id> best_id = GetBestId(*bsh.GetCompleteBioseq());
            if (best_id) {
                pnt.SetId().Assign(*best_id);
            }
        }
    }
}
 
 
static void UpgradeSeqLocId(CSeq_interval& interval, CScope& scope)
{
    if (interval.IsSetId()) {
        CBioseq_Handle bsh = scope.GetBioseqHandle(interval.GetId());
        if (bsh) {
            CConstRef<CSeq_id> best_id = GetBestId(*bsh.GetCompleteBioseq());
            if (best_id) {
                interval.SetId().Assign(*best_id);
            }
        }
    }
}
 
 
static void UpgradeSeqLocId(CSeq_loc& loc, CScope& scope)
{
    switch (loc.Which()) {
        case CSeq_loc::e_Bond:
            if (loc.GetBond().IsSetA()) {
                UpgradeSeqLocId(loc.SetBond().SetA(), scope);
            }
            if (loc.GetBond().IsSetB()) {
                UpgradeSeqLocId(loc.SetBond().SetB(), scope);
            }
            break;
        case CSeq_loc::e_Equiv:
            for (auto it: loc.SetEquiv().Set()) {
                UpgradeSeqLocId(*it, scope);
            }
            break;
        case CSeq_loc::e_Int:
            UpgradeSeqLocId(loc.SetInt(), scope);
            break;
 
        case CSeq_loc::e_Mix:
            for (auto it: loc.SetMix().Set()) {
                UpgradeSeqLocId(*it, scope);
            }
            break;
        case CSeq_loc::e_Packed_int:
            for (auto it: loc.SetPacked_int().Set()) {
                UpgradeSeqLocId(*it, scope);
            }
            break;
        case CSeq_loc::e_Packed_pnt:
            if (loc.GetPacked_pnt().IsSetId()) {
                CBioseq_Handle bsh = scope.GetBioseqHandle(loc.GetPacked_pnt().GetId());
                if (bsh) {
                    CConstRef<CSeq_id> best_id = GetBestId(*bsh.GetCompleteBioseq());
                    if (best_id) {
                        loc.SetPacked_pnt().SetId().Assign(*best_id);
                    }
                }
            }
            break;
        case CSeq_loc::e_Pnt:
            UpgradeSeqLocId(loc.SetPnt(), scope);
            break;
        case CSeq_loc::e_Whole:
            {
                CBioseq_Handle bsh = scope.GetBioseqHandle(loc.GetPacked_pnt().GetId());
                if (bsh) {
                    CConstRef<CSeq_id> best_id = GetBestId(*bsh.GetCompleteBioseq());
                    if (best_id) {
                        loc.SetWhole().Assign(*best_id);
                    }
                }
            }
            break;
        case CSeq_loc::e_Null:
        case CSeq_loc::e_Empty:
        case CSeq_loc::e_Feat:
        case CSeq_loc::e_not_set:
            break;
    }
}
 
 
static string GetLocusTagForFeature(const CSeq_feat& seq_feat, CScope& scope)
{
    string tag(kEmptyStr);
    if (seq_feat.GetData().IsGene()) {
        const CGene_ref& gene = seq_feat.GetData().GetGene();
        tag = (gene.CanGetLocus_tag()) ? gene.GetLocus_tag() : kEmptyStr;
    }
    else {
        const CGene_ref* gene = seq_feat.GetGeneXref();
        if (gene) {
            tag = (gene->CanGetLocus_tag()) ? gene->GetLocus_tag() : kEmptyStr;
        }
        else {
            CConstRef<CSeq_feat> gene = sequence::GetGeneForFeature(seq_feat, scope);
            if (gene.NotEmpty()) {
                tag = (gene->GetData().GetGene().CanGetLocus_tag()) ? gene->GetData().GetGene().GetLocus_tag() : kEmptyStr;
            }
        }
    }
    return tag;
}
 
 
static string GetProduct(const CProt_ref& prot_ref)
{
    string rval;
    if (prot_ref.CanGetName() && !prot_ref.GetName().empty()) {
        rval = prot_ref.GetName().front();
    }
    return rval;
}
 
 
static string GetProductForCDS(const CSeq_feat& cds, CScope& scope)
{
    // use protein xref if available
    const CProt_ref* prot = cds.GetProtXref();
    if (prot) {
        return GetProduct(*prot);
    }
 
    // should be the longest protein feature on the bioseq pointed by the cds.GetProduct()
    if (cds.IsSetProduct()) {
        CConstRef <CSeq_feat> prot_seq_feat = sequence::GetBestOverlappingFeat(cds.GetProduct(),
            CSeqFeatData::e_Prot,
            sequence::eOverlap_Contains,
            scope);
        if (prot_seq_feat && prot_seq_feat->GetData().IsProt()) {
            return GetProduct(prot_seq_feat->GetData().GetProt());
        }
    }
    return (kEmptyStr);
}
 
 
static string GetSeqLocDescription(const CSeq_loc& loc, CScope& scope)
{
    string location;
 
    CRef<CSeq_loc> cpy(new CSeq_loc());
    cpy->Assign(loc);
    UpgradeSeqLocId(*cpy, scope);
    cpy->GetLabel(&location);
    return location;
}
 
 
static void GetTextObjectDescription(const CSeq_feat& seq_feat, CScope& scope, string &label, string &location, string &locus_tag)
{
    location = GetSeqLocDescription(seq_feat.GetLocation(), scope);
    label = seq_feat.GetData().GetKey();
    locus_tag = GetLocusTagForFeature(seq_feat, scope);
}
 
 
static string GetTextObjectDescription(const CSeq_feat& seq_feat, CScope& scope, const string& product)
{
    string location;
    string label;
    string locus_tag;
    GetTextObjectDescription(seq_feat, scope, label, location, locus_tag);
    string rval = label + "\t" + product + "\t" + location + "\t" + locus_tag; // + "\n";
    return rval;
}
 
 
void GetTextObjectDescription(const CSeq_feat& seq_feat, CScope& scope, string &label, string &context, string &location, string &locus_tag)
{
    if (seq_feat.GetData().IsProt()) {
        CConstRef <CBioseq> bioseq = sequence::GetBioseqFromSeqLoc(seq_feat.GetLocation(), scope).GetCompleteBioseq();
        if (bioseq) {
            const CSeq_feat* cds = sequence::GetCDSForProduct(*bioseq, &scope);
            if (cds) {
                context = GetProduct(seq_feat.GetData().GetProt());
                GetTextObjectDescription(*cds, scope, label, location, locus_tag);
                return;
            }
        }
    }
    else if (seq_feat.GetData().IsBiosrc() && seq_feat.GetData().GetBiosrc().IsSetOrg()) {
        const COrg_ref& org = seq_feat.GetData().GetBiosrc().GetOrg();
        label = (org.CanGetTaxname() ? org.GetTaxname()
            : (org.CanGetCommon() ? org.GetCommon() : kEmptyStr));
        location = GetSeqLocDescription(seq_feat.GetLocation(), scope);
        locus_tag.clear();
        return;
    }
 
    GetTextObjectDescription(seq_feat, scope, label, location, locus_tag);
    context.clear();
    if (seq_feat.GetData().IsCdregion()) {
        context = GetProductForCDS(seq_feat, scope);
        if (NStr::IsBlank(context)) {
            GetSeqFeatLabel(seq_feat, context);
        }
    }
    else if (seq_feat.GetData().IsPub()) {
        seq_feat.GetData().GetPub().GetPub().GetLabel(&context);
    }
    else if (seq_feat.GetData().IsGene()) {
        if (seq_feat.GetData().GetGene().CanGetLocus() &&
            !NStr::IsBlank(seq_feat.GetData().GetGene().GetLocus())) {
            context = seq_feat.GetData().GetGene().GetLocus();
        }
        else if (seq_feat.GetData().GetGene().CanGetDesc()) {
            context = seq_feat.GetData().GetGene().GetDesc();
        }
        else context = GetLocusTagForFeature(seq_feat, scope);
    }
    else GetSeqFeatLabel(seq_feat, context);
}
 
 
string GetTextObjectDescription(const CSeq_feat& sf, CScope& scope)
{
    string type;
    string location;
    string context;
    string locus_tag;
    GetTextObjectDescription(sf, scope, type, context, location, locus_tag);
    return type + "\t" + context + "\t" + location + "\t" + locus_tag;
}
 
 
string GetTextObjectDescription(const CSeqdesc& sd, CScope& scope)
{
    string label(kEmptyStr);
    switch (sd.Which()) {
        case CSeqdesc::e_Comment: return (sd.GetComment());
        case CSeqdesc::e_Region: return (sd.GetRegion());
        case CSeqdesc::e_Het: return (sd.GetHet());
        case CSeqdesc::e_Title: return (sd.GetTitle());
        case CSeqdesc::e_Name: return (sd.GetName());
        case CSeqdesc::e_Create_date:
            sd.GetCreate_date().GetDate(&label);
            break;
        case CSeqdesc::e_Update_date:
            sd.GetUpdate_date().GetDate(&label);
            break;
        case CSeqdesc::e_Org:
            {
                const COrg_ref& org = sd.GetOrg();
                label = (org.CanGetTaxname() ? org.GetTaxname() : (org.CanGetCommon() ? org.GetCommon() : kEmptyStr));
            }
            break;
        case CSeqdesc::e_Pub:
            sd.GetPub().GetPub().GetLabel(&label);
            break;
        case CSeqdesc::e_User:
            {
                const CUser_object& uop = sd.GetUser();
                label = (uop.CanGetClass() ? uop.GetClass() : (uop.GetType().IsStr() ? uop.GetType().GetStr() : kEmptyStr));
            }
            break;
        case CSeqdesc::e_Method:
            label = (ENUM_METHOD_NAME(EGIBB_method)()->FindName(sd.GetMethod(), true));
            break;
        case CSeqdesc::e_Mol_type:
            label = (ENUM_METHOD_NAME(EGIBB_mol)()->FindName(sd.GetMol_type(), true));
            break;
        case CSeqdesc::e_Modif:
            for (auto it: sd.GetModif()) {
                label += ENUM_METHOD_NAME(EGIBB_mod)()->FindName(it, true) + ", ";
            }
            label = label.substr(0, label.size() - 2);
            break;
        case CSeqdesc::e_Source:
            {
                const COrg_ref& org = sd.GetSource().GetOrg();
                label = (org.CanGetTaxname() ? org.GetTaxname() : (org.CanGetCommon() ? org.GetCommon() : kEmptyStr));
            }
            break;
        case CSeqdesc::e_Maploc:
            sd.GetMaploc().GetLabel(&label);
            break;
        case CSeqdesc::e_Molinfo:
            sd.GetMolinfo().GetLabel(&label);
            break;
        case CSeqdesc::e_Dbxref:
            sd.GetDbxref().GetLabel(&label);
            break;
        default:
            break;
    }
    return label;
}
 
 
string GetTextObjectDescription(const CBioseq& bs, CScope& scope)
{
    string rval;
    CConstRef<CSeq_id> id = GetBestId(bs);
    id->GetLabel(&rval, CSeq_id::eContent);
    return rval;
}
 
 
string GetTextObjectDescription(const CBioseq_set& bs, CScope& scope)
{
    return GetTextObjectDescription(scope.GetBioseq_setHandle(bs));
}
 
 
END_SCOPE(edit)
END_SCOPE(objects)
END_NCBI_SCOPE