validerror_format.cpp

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/* $Id: validerror_format.cpp 102322 2024-04-23 12:29:28Z foleyjp $
 * ===========================================================================
 *
 *                            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:  Jonathan Kans, Clifford Clausen, Aaron Ucko.......
 *
 * File Description:
 *   Validates CSeq_entries and CSeq_submits
 *
 */
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <serial/serialbase.hpp>
#include <objects/submit/Seq_submit.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/pub/Pub_equiv.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seqfeat/Feat_id.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/OrgMod.hpp>
#include <objects/general/User_object.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/validator/validerror_format.hpp>
#include <objtools/validator/validerror_suppress.hpp>
#include <objtools/validator/utilities.hpp>
#include <util/static_map.hpp>
 
 
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
BEGIN_SCOPE(validator)
USING_SCOPE(sequence);
 
 
// *********************** CValidErrorFormat implementation **********************
 
 
//LCOV_EXCL_START
//used by Genome Workbench to create submitter report,
//not used by asnvalidate
CValidErrorFormat::CValidErrorFormat(CObjectManager& objmgr) :
    m_ObjMgr(&objmgr)
{
}
 
 
CValidErrorFormat::~CValidErrorFormat()
{
}
 
 
ESubmitterFormatErrorGroup CValidErrorFormat::GetSubmitterFormatErrorGroup(CValidErrItem::TErrIndex err_code) const
{
    ESubmitterFormatErrorGroup rval = eSubmitterFormatErrorGroup_Default;
 
    switch(err_code) {
    case eErr_SEQ_FEAT_NotSpliceConsensus:
    case eErr_SEQ_FEAT_NotSpliceConsensusDonor:
    case eErr_SEQ_FEAT_NotSpliceConsensusAcceptor:
    case eErr_SEQ_FEAT_RareSpliceConsensusDonor:
    case eErr_SEQ_FEAT_NotSpliceConsensusAcceptorTerminalIntron:
    case eErr_SEQ_FEAT_NotSpliceConsensusDonorTerminalIntron:
        rval = eSubmitterFormatErrorGroup_ConsensusSplice;
        break;
    case eErr_SEQ_FEAT_BadEcNumberFormat:
        rval = eSubmitterFormatErrorGroup_BadEcNumberFormat;
        break;
    case eErr_SEQ_FEAT_BadEcNumberValue:
    case eErr_SEQ_FEAT_DeletedEcNumber:
    case eErr_SEQ_FEAT_ReplacedEcNumber:
    case eErr_SEQ_FEAT_SplitEcNumber:
        rval = eSubmitterFormatErrorGroup_BadEcNumberValue;
        break;
    case eErr_SEQ_FEAT_EcNumberProblem:
        rval = eSubmitterFormatErrorGroup_BadEcNumberProblem;
        break;
    case eErr_SEQ_DESCR_BadSpecificHost:
        rval = eSubmitterFormatErrorGroup_BadSpecificHost;
        break;
    case eErr_SEQ_DESCR_BadInstitutionCode:
        rval = eSubmitterFormatErrorGroup_BadInstitutionCode;
        break;
    case eErr_SEQ_DESCR_LatLonCountry:
    case eErr_SEQ_DESCR_LatLonWater:
        rval = eSubmitterFormatErrorGroup_LatLonCountry;
        break;
    default:
        break;
    }
    return rval;
}
 
 
string CValidErrorFormat::GetSubmitterFormatErrorGroupTitle(CValidErrItem::TErrIndex err_code) const
{
    string rval;
    switch(err_code) {
    case eErr_SEQ_FEAT_NotSpliceConsensus:
    case eErr_SEQ_FEAT_NotSpliceConsensusDonor:
    case eErr_SEQ_FEAT_NotSpliceConsensusAcceptor:
    case eErr_SEQ_FEAT_RareSpliceConsensusDonor:
        rval = "Not Splice Consensus";
        break;
    case eErr_SEQ_FEAT_BadEcNumberFormat:
        rval = "EC Number Format";
        break;
    case eErr_SEQ_FEAT_BadEcNumberValue:
    case eErr_SEQ_FEAT_DeletedEcNumber:
    case eErr_SEQ_FEAT_ReplacedEcNumber:
    case eErr_SEQ_FEAT_SplitEcNumber:
        rval = "EC Number Value";
        break;
    case eErr_SEQ_FEAT_EcNumberProblem:
        rval = "EC Number Problem";
        break;
    case eErr_SEQ_DESCR_BadSpecificHost:
        rval = "Bad Specific-host Values";
        break;
    case eErr_SEQ_DESCR_BadInstitutionCode:
        rval = "Bad Institution Codes";
        break;
    case eErr_SEQ_DESCR_LatLonCountry:
    case eErr_SEQ_DESCR_LatLonWater:
        rval = "LatLonCountry Errors";
        break;
    default:
        rval = CValidErrItem::ConvertErrCode(err_code);
        break;
    }
 
    return rval;
}
 
 
string CValidErrorFormat::FormatForSubmitterReport(const CValidErrItem& error, CScope& scope) const
{
    string rval;
 
    switch (error.GetErrIndex()) {
    case eErr_SEQ_FEAT_NotSpliceConsensus:
    case eErr_SEQ_FEAT_NotSpliceConsensusDonor:
    case eErr_SEQ_FEAT_NotSpliceConsensusAcceptor:
    case eErr_SEQ_FEAT_RareSpliceConsensusDonor:
    case eErr_SEQ_FEAT_NotSpliceConsensusAcceptorTerminalIntron:
    case eErr_SEQ_FEAT_NotSpliceConsensusDonorTerminalIntron:
        rval = x_FormatConsensusSpliceForSubmitterReport(error);
        break;
    case eErr_SEQ_FEAT_BadEcNumberFormat:
    case eErr_SEQ_FEAT_BadEcNumberValue:
    case eErr_SEQ_FEAT_EcNumberProblem:
    case eErr_SEQ_FEAT_DeletedEcNumber:
    case eErr_SEQ_FEAT_ReplacedEcNumber:
    case eErr_SEQ_FEAT_SplitEcNumber:
        rval = x_FormatECNumberForSubmitterReport(error, scope);
        break;
    case eErr_SEQ_DESCR_BadSpecificHost:
        rval = x_FormatBadSpecificHostForSubmitterReport(error);
        break;
    case eErr_SEQ_DESCR_BadInstitutionCode:
        rval = x_FormatBadInstCodeForSubmitterReport(error);
        break;
    case eErr_SEQ_DESCR_LatLonCountry:
    case eErr_SEQ_DESCR_LatLonWater:
        rval = x_FormatLatLonCountryForSubmitterReport(error);
        break;
    default:
        rval = x_FormatGenericForSubmitterReport(error, scope);
        break;
    }
 
    return rval;
}
 
 
string CValidErrorFormat::x_FormatConsensusSpliceForSubmitterReport(const CValidErrItem& error) const
{
    string rval;
    if (!error.IsSetMsg() || NStr::IsBlank(error.GetMsg())) {
        return rval;
    }
    string msg = error.GetMsg();
    if (NStr::Find(msg, "(AG) not found") != string::npos) {
        rval = "AG";
    }
    else if (NStr::Find(msg, "(GT) not found") != string::npos) {
        rval = "GT";
    } else if (NStr::Find(msg, "(AT-AC) found instead of (GT-AG)") != string::npos) {
        rval = "(AT-AC) instead of (GT-AG)";
    } else if (NStr::Find(msg, "(GC-AG) found instead of (GT-AG)") != string::npos) {
        rval = "(GC-AG) instead of (GT-AG)";
    }
    if (NStr::IsBlank(rval)) {
        return rval;
    }
 
    size_t position_pos = NStr::Find(msg, "ending at position ");
    size_t other_clue = NStr::Find(msg, "and before exon");
    if (position_pos == string::npos || other_clue == string::npos) {
        position_pos = NStr::Find(msg, "position ");
        if (position_pos != string::npos) {
            string pos_str = msg.substr(position_pos);
            long int pos;
            if (sscanf(pos_str.c_str(), "position %ld of ", &pos) == 1) {
                rval += " at " + NStr::NumericToString(pos);
                size_t seq_pos = NStr::Find(pos_str, " of ");
                if (seq_pos != string::npos) {
                    rval = pos_str.substr(seq_pos + 4) + "\t" + rval;
                }
            }
        }
    } else {
        string pos_str = msg.substr(position_pos);
        long int pos1, pos2;
        if (sscanf(pos_str.c_str(), "ending at position %ld and before exon starting at position %ld of ", &pos1, &pos2) == 2) {
            rval += " at " + NStr::NumericToString(pos1) + ", " + NStr::NumericToString(pos2);
            size_t seq_pos = NStr::Find(pos_str, " of ");
            if (seq_pos != string::npos) {
                rval = pos_str.substr(seq_pos + 4) + "\t" + rval;
            }
        }
    }
 
    string obj_desc = error.GetObjDesc();
    size_t type_pos = NStr::Find(obj_desc, "FEATURE: ");
    if (type_pos != string::npos) {
        obj_desc = obj_desc.substr(type_pos + 9);
        size_t space_pos = NStr::Find(obj_desc, ":");
        if (space_pos != string::npos) {
            obj_desc = obj_desc.substr(0, space_pos);
        }
    }
 
    rval = obj_desc + "\t" + rval;
 
    return rval;
}
 
 
void RemovePrefix(string& str, const string& prefix)
{
    size_t type_pos = NStr::Find(str, prefix);
    if (type_pos != string::npos) {
        str = str.substr(type_pos + prefix.length());
    }
}
 
void RemoveSuffix(string& str, const string& suffix)
{
    size_t type_pos = NStr::Find(str, suffix);
    if (type_pos != string::npos) {
        str = str.substr(0, type_pos);
    }
}
 
 
string CValidErrorFormat::x_FormatGenericForSubmitterReport(const CValidErrItem& error, CScope& scope) const
{
    string obj_desc = error.GetObjDesc();
    if (NStr::StartsWith(obj_desc, "FEATURE") && error.IsSetObj_content()) {
        obj_desc = error.GetObj_content();
        NStr::ReplaceInPlace(obj_desc, ":", "\t", 0, 1);
        // Add feature location part of label
        if (error.IsSetLocation()) {
            obj_desc += "\t" + error.GetLocation();
        }
        if (error.IsSetLocus_tag()) {
            obj_desc += "\t" + error.GetLocus_tag();
        } else if (error.IsSetObject() && error.GetObject().GetThisTypeInfo() == CSeq_feat:: GetTypeInfo()) {
            const CSeq_feat* sf = static_cast<const CSeq_feat*>(&(error.GetObject()));
            if (sf) {
                obj_desc += "\t" + x_GetLocusTag(*sf, scope);
            }
        }
    } else {
        RemovePrefix(obj_desc, "DESCRIPTOR: ");
        RemovePrefix(obj_desc, "BioSrc: ");
        RemoveSuffix(obj_desc, " BIOSEQ: ");
        RemoveSuffix(obj_desc, " BIOSEQ-SET: ");
 
        NStr::ReplaceInPlace(obj_desc, ":", "\t", 0, 1);
        size_t close_pos = NStr::Find(obj_desc, "]");
        if (close_pos != string::npos) {
            obj_desc = obj_desc.substr(0, close_pos);
            NStr::ReplaceInPlace(obj_desc, "[", "\t");
        }
    }
    string rval = error.GetAccession() + ":" + obj_desc;
 
    return rval;
}
 
 
string CValidErrorFormat::x_FormatECNumberForSubmitterReport(const CValidErrItem& error, CScope& scope) const
{
    string rval;
    string ec_numbers;
    string prot_name;
    string locus_tag;
 
    // want: accession number for sequence, ec numbers, locus tag, protein name
 
    if (error.GetObject().GetThisTypeInfo() != CSeq_feat::GetTypeInfo()) {
        return rval;
    }
    const CSeq_feat* feat = static_cast<const CSeq_feat*>(&(error.GetObject()));
    if (!feat) {
        return rval;
    }
 
    // look for EC number in quals
    if (feat->IsSetQual()) {
        ITERATE(CSeq_feat::TQual, it, feat->GetQual()) {
            if ((*it)->IsSetQual() &&
                NStr::EqualNocase((*it)->GetQual(), "EC_number") &&
                (*it)->IsSetVal() &&
                !NStr::IsBlank((*it)->GetVal())) {
                if (!NStr::IsBlank(ec_numbers)) {
                    ec_numbers += ";";
                }
                ec_numbers += (*it)->GetVal();
            }
        }
    }
    // look for EC number in prot-ref
    if (feat->IsSetData() && feat->GetData().IsProt() &&
        feat->GetData().GetProt().IsSetEc()) {
        ITERATE(CProt_ref::TEc, it, feat->GetData().GetProt().GetEc()) {
            if (!NStr::IsBlank(ec_numbers)) {
                    ec_numbers += ";";
            }
            ec_numbers += *it;
        }
    }
 
    if (NStr::IsBlank(ec_numbers)) {
        ec_numbers = "Blank EC number";
    }
 
    // look for protein name
    if (feat->IsSetData() && feat->GetData().IsProt() &&
        feat->GetData().GetProt().IsSetName() &&
        !feat->GetData().GetProt().GetName().empty()) {
        prot_name = feat->GetData().GetProt().GetName().front();
    }
 
    // get locus tag
    CConstRef <CSeq_feat> gene = sequence::GetGeneForFeature(*feat, scope);
    if (gene && gene->GetData().GetGene().IsSetLocus_tag()) {
        locus_tag = gene->GetData().GetGene().GetLocus_tag();
    }
 
    rval = error.GetAccnver() + "\t" + ec_numbers + "\t" + locus_tag + "\t" + prot_name;
    return rval;
}
 
 
string s_GetSpecificHostFromBioSource(const CBioSource& biosrc)
{
    string rval;
 
    if (biosrc.IsSetOrg() &&
        biosrc.GetOrg().IsSetOrgname() &&
        biosrc.GetOrg().GetOrgname().IsSetMod()) {
        ITERATE(COrgName::TMod, it, biosrc.GetOrg().GetOrgname().GetMod()) {
            if ((*it)->IsSetSubtype() &&
                (*it)->GetSubtype() == COrgMod::eSubtype_nat_host &&
                (*it)->IsSetSubname() &&
                !NStr::IsBlank((*it)->GetSubname())) {
                if (!NStr::IsBlank(rval)) {
                    rval += ";";
                }
                rval += (*it)->GetSubname();
            }
        }
    }
    return rval;
}
 
 
string CValidErrorFormat::x_FormatBadSpecificHostForSubmitterReport(const CValidErrItem& error) const
{
    string rval;
    string spec_host;
    const string kAlternateName = "Specific host value is alternate name: ";
    if (NStr::StartsWith(error.GetMsg(), kAlternateName)) {
        spec_host = error.GetMsg().substr(kAlternateName.length());
    } else if (error.GetObject().GetThisTypeInfo() == CSeqdesc::GetTypeInfo()) {
        const CSeqdesc* desc = static_cast<const CSeqdesc *>(&(error.GetObject()));
        if (desc && desc->IsSource()) {
            spec_host = s_GetSpecificHostFromBioSource(desc->GetSource());
        }
    } else if (error.GetObject().GetThisTypeInfo() == CSeq_feat::GetTypeInfo()) {
        const CSeq_feat* feat = static_cast<const CSeq_feat *>(&(error.GetObject()));
        if (feat && feat->IsSetData() && feat->GetData().IsBiosrc()) {
            spec_host = s_GetSpecificHostFromBioSource(feat->GetData().GetBiosrc());
        }
    }
 
    if (!NStr::IsBlank(spec_host)) {
        rval = error.GetAccession() + "\t" + spec_host;
    }
 
    return rval;
}
 
 
string s_GetInstCodeFromBioSource(const CBioSource& biosrc)
{
    string rval;
 
    if (biosrc.IsSetOrg() &&
        biosrc.GetOrg().IsSetOrgname() &&
        biosrc.GetOrg().GetOrgname().IsSetMod()) {
        ITERATE(COrgName::TMod, it, biosrc.GetOrg().GetOrgname().GetMod()) {
            if ((*it)->IsSetSubtype() &&
                ((*it)->GetSubtype() == COrgMod::eSubtype_bio_material ||
                 (*it)->GetSubtype() == COrgMod::eSubtype_culture_collection ||
                 (*it)->GetSubtype() == COrgMod::eSubtype_specimen_voucher) &&
                (*it)->IsSetSubname() &&
                !NStr::IsBlank((*it)->GetSubname())) {
                size_t pos = NStr::Find((*it)->GetSubname(), ":");
                if (pos != string::npos) {
                    string code = (*it)->GetSubname().substr(0, pos);
                    if (!NStr::IsBlank(code)) {
                        if (!NStr::IsBlank(rval)) {
                            rval += ";";
                        }
                        rval += code;
                    }
                }
            }
        }
    }
    return rval;
}
 
 
string CValidErrorFormat::x_FormatBadInstCodeForSubmitterReport(const CValidErrItem& error) const
{
    string rval;
 
    string codes;
    if (error.GetObject().GetThisTypeInfo() == CSeqdesc::GetTypeInfo()) {
        const CSeqdesc* desc = static_cast<const CSeqdesc *>(&(error.GetObject()));
        if (desc && desc->IsSource()) {
            codes = s_GetInstCodeFromBioSource(desc->GetSource());
        }
    }
    else if (error.GetObject().GetThisTypeInfo() == CSeq_feat::GetTypeInfo()) {
        const CSeq_feat* feat = static_cast<const CSeq_feat *>(&(error.GetObject()));
        if (feat && feat->IsSetData() && feat->GetData().IsBiosrc()) {
            codes = s_GetInstCodeFromBioSource(feat->GetData().GetBiosrc());
        }
    }
 
    if (!NStr::IsBlank(codes)) {
        rval = error.GetAccession() + "\t" + codes;
    }
 
    return rval;
}
 
 
string CValidErrorFormat::FormatForSubmitterReport(const CValidError& errors, CScope& scope, CValidErrItem::TErrIndex err_code) const
{
    string rval;
    for ( CValidError_CI vit(errors); vit; ++vit) {
        if (err_code == vit->GetErrIndex()) {
            string this_val = FormatForSubmitterReport(*vit, scope);
            if (!NStr::IsBlank(this_val)) {
                if (NStr::IsBlank(rval)) {
                    rval += GetSubmitterFormatErrorGroupTitle(err_code) + "\n";
                }
                rval += this_val + "\n";
            }
        }
    }
    return rval;
}
 
 
string CValidErrorFormat::FormatCategoryForSubmitterReport
    (const CValidError& errors, CScope& scope, ESubmitterFormatErrorGroup grp) const
{
    string rval;
    for ( CValidError_CI vit(errors); vit; ++vit) {
        CValidErrItem::TErrIndex err_code = vit->GetErrIndex();
        if (GetSubmitterFormatErrorGroup(err_code) == grp) {
            string this_val = FormatForSubmitterReport(*vit, scope);
            if (!NStr::IsBlank(this_val)) {
                if (NStr::IsBlank(rval)) {
                    rval += GetSubmitterFormatErrorGroupTitle(err_code) + "\n";
                }
                rval += this_val + "\n";
            }
        }
    }
    return rval;
}
 
 
string CValidErrorFormat::x_FormatLatLonCountryForSubmitterReport(const CValidErrItem& error) const
{
    string rval = error.GetAccession() + ":" + error.GetMsg();
    return rval;
}
 
 
vector<CValidErrItem::TErrIndex> CValidErrorFormat::GetListOfErrorCodes(const CValidError& errors) const
{
    vector<CValidErrItem::TErrIndex> list;
 
    for (CValidError_CI vit(errors); vit; ++vit) {
        list.push_back(vit->GetErrIndex());
    }
    sort(list.begin(), list.end());
    list.erase(unique(list.begin(), list.end()), list.end());
    return list;
}
 
 
vector<string> CValidErrorFormat::FormatCompleteSubmitterReport(const CValidError& errors, CScope& scope) const
{
    vector<string> list;
 
    // first, do special categories
    for (unsigned int t = eSubmitterFormatErrorGroup_ConsensusSplice; t < eSubmitterFormatErrorGroup_Default; ++t) {
        string this_val = FormatCategoryForSubmitterReport(errors, scope, (ESubmitterFormatErrorGroup)t);
        if (!NStr::IsBlank(this_val)) {
            list.push_back(this_val);
        }
    }
 
    // now do errors not in special categories
    vector<CValidErrItem::TErrIndex> codes = GetListOfErrorCodes(errors);
    ITERATE(vector<CValidErrItem::TErrIndex>, it, codes) {
        if (GetSubmitterFormatErrorGroup(*it) == eSubmitterFormatErrorGroup_Default) {
            string this_val = FormatForSubmitterReport(errors, scope, *it);
            if (!NStr::IsBlank(this_val)) {
                list.push_back(this_val);
            }
        }
    }
    return list;
}
//LCOV_EXCL_STOP
 
 
static string s_GetFeatureIdLabel (const CObject_id& object_id)
{
    string feature_id;
    if (object_id.IsId()) {
        feature_id = NStr::IntToString(object_id.GetId());
    } else if (object_id.IsStr()) {
        feature_id = object_id.GetStr();
    }
    return feature_id;
}
 
 
string CValidErrorFormat::GetFeatureIdLabel (const CFeat_id& feat_id)
{
    string feature_id;
    if (feat_id.IsLocal()) {
        feature_id = s_GetFeatureIdLabel(feat_id.GetLocal());
    } else if (feat_id.IsGeneral()) {
        if (feat_id.GetGeneral().IsSetDb()) {
            feature_id += feat_id.GetGeneral().GetDb();
        }
        feature_id += ":";
        if (feat_id.GetGeneral().IsSetTag()) {
            feature_id += s_GetFeatureIdLabel (feat_id.GetGeneral().GetTag());
        }
    }
    return feature_id;
}
 
 
string CValidErrorFormat::GetFeatureIdLabel(const CSeq_feat& ft)
{
    string feature_id;
    if (ft.IsSetId()) {
        feature_id = CValidErrorFormat::GetFeatureIdLabel(ft.GetId());
    } else if (ft.IsSetIds()) {
        ITERATE(CSeq_feat::TIds, id_it, ft.GetIds()) {
            feature_id = CValidErrorFormat::GetFeatureIdLabel((**id_it));
            if (!NStr::IsBlank(feature_id)) {
                break;
            }
        }
    }
    return feature_id;
}
 
 
static void s_FixBioseqLabelProblems (string& str)
{
    size_t pos = NStr::Find(str, ",");
    if (pos != string::npos && str.c_str()[pos + 1] != 0 && str.c_str()[pos + 1] != ' ') {
        str = str.substr(0, pos + 1) + " " + str.substr(pos + 1);
    }
    pos = NStr::Find(str, "=");
    if (pos != string::npos && str.c_str()[pos + 1] != 0 && str.c_str()[pos + 1] != ' ') {
        str = str.substr(0, pos + 1) + " " + str.substr(pos + 1);
    }
}
 
 
 
static string s_GetOrgRefContentLabel (const COrg_ref& org)
{
    string content;
    if (org.IsSetTaxname()) {
        content = org.GetTaxname();
    } else if (org.IsSetCommon()) {
        content = org.GetCommon();
    } else if (org.IsSetDb() && !org.GetDb().empty()) {
        org.GetDb().front()->GetLabel(&content);
    }
    return content;
}
 
 
static string s_GetBioSourceContentLabel (const CBioSource& bsrc)
{
    string content;
    if (bsrc.IsSetOrg()) {
        content = s_GetOrgRefContentLabel(bsrc.GetOrg());
    }
    return content;
}
 
 
static string s_GetFeatureContentLabelExtras (const CSeq_feat& feat)
{
    string tlabel;
 
    // Put Seq-feat qual into label
    if (feat.IsSetQual()) {
        string prefix("/");
        ITERATE(CSeq_feat::TQual, it, feat.GetQual()) {
            tlabel += prefix + (**it).GetQual();
            prefix = " ";
            if (!(**it).GetVal().empty()) {
                tlabel += "=" + (**it).GetVal();
            }
        }
    }
 
    // Put Seq-feat comment into label
    if (feat.IsSetComment()) {
        if (tlabel.empty()) {
            tlabel = feat.GetComment();
        } else {
            tlabel += "; " + feat.GetComment();
        }
    }
    return tlabel;
}
 
 
static string s_GetCdregionContentLabel (const CSeq_feat& feat, CRef<CScope> scope)
{
    string content;
 
    // Check that feature data is Cdregion
    if (!feat.GetData().IsCdregion()) {
        return content;
    }
 
    const CGene_ref* gref = nullptr;
    const CProt_ref* pref = nullptr;
 
    // Look for CProt_ref object to create a label from
    if (feat.IsSetXref()) {
        ITERATE ( CSeq_feat::TXref, it, feat.GetXref()) {
            const CSeqFeatXref& xref = **it;
            if ( !xref.IsSetData() ) {
                continue;
            }
 
            switch (xref.GetData().Which()) {
            case CSeqFeatData::e_Prot:
                pref = &xref.GetData().GetProt();
                break;
            case CSeqFeatData::e_Gene:
                gref = &xref.GetData().GetGene();
                break;
            default:
                break;
            }
        }
    }
 
    // Try and create a label from a CProt_ref in CSeqFeatXref in feature
    if (pref) {
        pref->GetLabel(&content);
        return content;
    }
 
    // Try and create a label from a CProt_ref in the feat product and
    // return if found
    if (feat.IsSetProduct()  &&  scope) {
        try {
            const CSeq_id& id = GetId(feat.GetProduct(), scope);
            CBioseq_Handle hnd = scope->GetBioseqHandle(id);
            if (hnd) {
                const CBioseq& seq = *hnd.GetCompleteBioseq();
 
                // Now look for a CProt_ref feature in seq and
                // if found call GetLabel() on the CProt_ref
                CTypeConstIterator<CSeqFeatData> it = ConstBegin(seq);
                for (;it; ++it) {
                    if (it->IsProt()) {
                        it->GetProt().GetLabel(&content);
                        return content;
                    }
                }
            }
        } catch (CObjmgrUtilException&) {}
    }
 
    // Try and create a label from a CGene_ref in CSeqFeatXref in feature
    if (gref) {
        gref->GetLabel(&content);
    }
 
    if (NStr::IsBlank(content)) {
        content = s_GetFeatureContentLabelExtras(feat);
    }
 
    return content;
}
 
 
string CValidErrorFormat::GetFeatureContentLabel (const CSeq_feat& feat, CRef<CScope> scope)
{
    string content_label;
 
    switch (feat.GetData().Which()) {
    case CSeqFeatData::e_Pub:
        content_label = "Cit: ";
        feat.GetData().GetPub().GetPub().GetLabel(&content_label);
        break;
    case CSeqFeatData::e_Biosrc:
        content_label = "Src: " + s_GetBioSourceContentLabel (feat.GetData().GetBiosrc());
        break;
    case CSeqFeatData::e_Imp: {
        feature::GetLabel(feat, &content_label, feature::fFGL_Both, scope);
        if (feat.GetData().GetImp().IsSetKey()) {
            string key = feat.GetData().GetImp().GetKey();
            string tmp = "[" + key + "]";
            if (NStr::StartsWith(content_label, tmp)) {
                content_label = key + content_label.substr(tmp.length());
            }
        }
    } break;
    case CSeqFeatData::e_Rna:
        feature::GetLabel(feat, &content_label, feature::fFGL_Both, scope);
        if (feat.GetData().GetSubtype() == CSeqFeatData::eSubtype_tRNA
            && NStr::Equal(content_label, "tRNA: tRNA")) {
            content_label = "tRNA: ";
        }
        break;
    case CSeqFeatData::e_Cdregion:
        content_label = "CDS: " + s_GetCdregionContentLabel(feat, scope);
        break;
    case CSeqFeatData::e_Prot:
        feature::GetLabel(feat, &content_label, feature::fFGL_Both, scope);
        if (feat.GetData().GetProt().IsSetProcessed()) {
            switch (feat.GetData().GetProt().GetProcessed()) {
            case CProt_ref::eProcessed_mature:
                content_label = "mat_peptide: " + content_label.substr(6);
                break;
            case CProt_ref::eProcessed_signal_peptide:
                content_label = "sig_peptide: " + content_label.substr(6);
                break;
            case CProt_ref::eProcessed_transit_peptide:
                content_label = "trans_peptide: " + content_label.substr(6);
                break;
            default:
                break;
            }
        }
        break;
    default:
        feature::GetLabel(feat, &content_label, feature::fFGL_Both, scope);
        break;
    }
    return content_label;
}
 
 
string CValidErrorFormat::GetFeatureBioseqLabel(const CSeq_feat& ft, CRef<CScope> scope, bool suppress_context)
{
    string desc;
    // Append label for bioseq of feature location
    if (!suppress_context && scope) {
        bool find_failed = false;
        try {
            CBioseq_Handle hnd;
            try {
                hnd = scope->GetBioseqHandle(ft.GetLocation());
            } catch (CException&) {
                CSeq_loc_CI li(ft.GetLocation());
                while (li && !hnd) {
                    hnd = scope->GetBioseqHandle(li.GetSeq_id());
                    ++li;
                }
            }
            if (hnd) {
                desc += CValidErrorFormat::GetBioseqLabel(hnd);
            }
        } catch (CObjMgrException& ex) {
            if (ex.GetErrCode() == CObjMgrException::eFindFailed) {
                find_failed = true;
            }
        } catch (const CException&) {
        } catch (const std::exception&) {
        };
        if (find_failed) {
            try {
                CSeq_loc_CI li(ft.GetLocation());
                CBioseq_Handle hnd = scope->GetBioseqHandle(li.GetSeq_id());
                if (hnd) {
                    desc += CValidErrorFormat::GetBioseqLabel(hnd);
                }
 
            } catch (const CException&) {
            } catch (const std::exception&) {
            };
        }
    }
    return desc;
}
 
 
string CValidErrorFormat::GetFeatureProductLocLabel(const CSeq_feat& ft, CRef<CScope> scope, bool suppress_context)
{
    string desc;
    // Append label for product of feature
    if (ft.IsSetProduct() && scope) {
        string loc_label;
        if (suppress_context) {
            CSeq_loc loc;
            loc.Assign(ft.GetProduct());
            ChangeSeqLocId(&loc, false, scope);
            loc_label = GetValidatorLocationLabel(loc, *scope);
        } else {
            loc_label = GetValidatorLocationLabel(ft.GetProduct(), *scope);
        }
        if (loc_label.size() > 800) {
            loc_label.replace(797, NPOS, "...");
        }
        if (!loc_label.empty()) {
            desc += "[";
            desc += loc_label;
            desc += "]";
        }
    }
    return desc;
}
 
 
string CValidErrorFormat::GetFeatureLocationLabel(const CSeq_feat& ft, CRef<CScope> scope, bool suppress_context)
{
    string loc_label;
    // Add feature location part of label
    if (ft.IsSetLocation() && scope) {
        if (suppress_context) {
            CSeq_loc loc;
            loc.Assign(ft.GetLocation());
            ChangeSeqLocId(&loc, false, scope);
            loc_label = GetValidatorLocationLabel(loc, *scope);
        } else {
            loc_label = GetValidatorLocationLabel(ft.GetLocation(), *scope);
        }
        if (loc_label.size() > 800) {
            loc_label.replace(795, NPOS, "...");
        }
    }
    return loc_label;
}
 
//LCOV_EXCL_START
//not used
string CValidErrorFormat::GetFeatureLabel(const CSeq_feat& ft, CRef<CScope> scope, bool suppress_context)
{
    // Add feature part of label
    string desc = "FEATURE: ";
    string content_label = CValidErrorFormat::GetFeatureContentLabel(ft, scope);
    desc += content_label;
 
    // Add feature ID part of label (if present)
    string feature_id = GetFeatureIdLabel(ft);
    if (!NStr::IsBlank(feature_id)) {
        desc += " <" + feature_id + "> ";
    }
 
    // Add feature location part of label
    string loc_label = GetFeatureLocationLabel(ft, scope, suppress_context);
    if (!NStr::IsBlank(loc_label)) {
        desc += " [" + loc_label + "]";
    }
 
    // Append label for bioseq of feature location
    string bioseq_label = GetFeatureBioseqLabel(ft, scope, suppress_context);
    if (!NStr::IsBlank(bioseq_label)) {
        desc += bioseq_label;
    }
 
    // Append label for product of feature
    string product_label = GetFeatureProductLocLabel(ft, scope, suppress_context);
    if (!NStr::IsBlank(product_label)) {
        desc += product_label;
    }
    return desc;
}
//LCOV_EXCL_STOP
 
 
string CValidErrorFormat::GetDescriptorContent (const CSeqdesc& ds)
{
    string content;
 
    switch (ds.Which()) {
    case CSeqdesc::e_Pub:
        content = "Pub: ";
        ds.GetPub().GetPub().GetLabel(&content);
        break;
    case CSeqdesc::e_Source:
        content = "BioSource: " + s_GetBioSourceContentLabel(ds.GetSource());
        break;
    case CSeqdesc::e_Modif:
        ds.GetLabel(&content, CSeqdesc::eBoth);
        if (NStr::StartsWith(content, "modif: ,")) {
            content = "Modifier: " + content.substr(8);
        }
        break;
    case CSeqdesc::e_Molinfo:
        ds.GetLabel(&content, CSeqdesc::eBoth);
        if (NStr::StartsWith(content, "molinfo: ,")) {
            content = "molInfo: " + content.substr(10);
        }
        break;
    case CSeqdesc::e_Comment:
        ds.GetLabel(&content, CSeqdesc::eBoth);
        if (NStr::StartsWith(content, "comment: ") && NStr::IsBlank(content.substr(9))) {
            content = "comment: ";
        }
        break;
    case CSeqdesc::e_User:
        content = "UserObj: ";
        if (ds.GetUser().IsSetClass()) {
            content += ds.GetUser().GetClass();
        } else if (ds.GetUser().IsSetType() && ds.GetUser().GetType().IsStr()) {
            content += ds.GetUser().GetType().GetStr();
        }
        break;
    default:
        ds.GetLabel(&content, CSeqdesc::eBoth);
        break;
    }
    // fix descriptor type names
    string first = content.substr(0, 1);
    NStr::ToUpper(first);
    content = first + content.substr(1);
    size_t colon_pos = NStr::Find(content, ":");
    if (colon_pos != string::npos) {
        size_t dash_pos = NStr::Find(content.substr(0, colon_pos), "-");
        if (dash_pos != string::npos) {
            string after_dash = content.substr(dash_pos + 1, 1);
            NStr::ToUpper (after_dash);
            content = content.substr(0, dash_pos) + after_dash + content.substr(dash_pos + 2);
        }
    }
    if (NStr::StartsWith(content, "BioSource:")) {
        content = "BioSrc:" + content.substr(10);
    } else if (NStr::StartsWith(content, "Modif:")) {
        content = "Modifier:" + content.substr(6);
    } else if (NStr::StartsWith(content, "Embl:")) {
        content = "EMBL:" + content.substr(5);
    } else if (NStr::StartsWith(content, "Pir:")) {
        content = "PIR:" + content.substr(4);
    }
    return content;
}
 
 
string CValidErrorFormat::GetDescriptorLabel(const CSeqdesc& ds, const CSeq_entry& ctx, CRef<CScope> scope, bool suppress_context)
{
    string desc("DESCRIPTOR: ");
 
    string content = CValidErrorFormat::GetDescriptorContent (ds);
 
    desc += content;
 
    desc += " ";
    if (ctx.IsSeq()) {
        AppendBioseqLabel(desc, ctx.GetSeq(), suppress_context);
    } else {
        desc += CValidErrorFormat::GetBioseqSetLabel(ctx.GetSet(), scope, suppress_context);
    }
   return desc;
}
 
 
string CValidErrorFormat::GetBioseqLabel (CBioseq_Handle bh)
{
    string desc;
 
    CBioseq_Handle::TBioseqCore bc = bh.GetBioseqCore();
    desc += " [";
    string bc_label;
    bc->GetLabel(&bc_label, CBioseq::eBoth);
    s_FixBioseqLabelProblems(bc_label);
    desc += bc_label;
    desc += "]";
    return desc;
}
 
 
string CValidErrorFormat::GetBioseqSetLabel(const CBioseq_set& st, CRef<CScope> /*dummy*/, bool suppress_context)
{
    return GetBioseqSetLabel(st, suppress_context);
}
 
 
string CValidErrorFormat::GetBioseqSetLabel(const CBioseq_set& st, bool suppress_context)
{
    const auto isSetClass = st.IsSetClass();
    suppress_context = suppress_context || !isSetClass;
 
    int version = 0;
    const string& accession = GetAccessionFromBioseqSet(st, &version);
    return GetBioseqSetLabel(accession, isSetClass ? st.GetClass() : CBioseq_set::eClass_not_set, suppress_context);
}
 
 
string CValidErrorFormat::GetBioseqSetLabel(const string& accession, CBioseq_set::EClass setClass, bool suppress_context)
{
    string str = "BIOSEQ-SET: ";
    if (!suppress_context) {
        const auto* tv = CBioseq_set::ENUM_METHOD_NAME(EClass)();
        const string& context = tv->FindName(setClass, true);
        str += context;
        str += ": ";
    }
 
    if(NStr::IsBlank(accession)) {
        str += "(No Bioseqs)";
        return str;
    }
 
    string temporary(accession); // create modifiable copy of accession
    s_FixBioseqLabelProblems(temporary);
    str += temporary;
    return str;
}
 
//LCOV_EXCL_START
//not used
string CValidErrorFormat::GetObjectLabel(const CObject& obj, const CSeq_entry& ctx, CRef<CScope> scope, bool suppress_context)
{
    string label = "Unknown object";
 
    const CSeq_feat* ft = dynamic_cast<const CSeq_feat*>(&obj);
    const CSeqdesc* ds = dynamic_cast<const CSeqdesc*>(&obj);
    const CBioseq* b = dynamic_cast<const CBioseq*>(&obj);
    const CBioseq_set* set = dynamic_cast<const CBioseq_set*>(&obj);
 
    if (ft) {
        label = GetFeatureLabel(*ft, scope, suppress_context);
    } else if (ds) {
        label = GetDescriptorLabel(*ds, ctx, scope, suppress_context);
    } else if (b) {
        label = GetBioseqLabel(scope->GetBioseqHandle(*b));
    } else if (set) {
        label = GetBioseqSetLabel(*set, suppress_context);
    }
    return label;
}
//LCOV_EXCL_STOP
 
 
static const string kSuppressFieldLabel = "Suppress";
 
static bool s_IsSuppressField (const CUser_field& field)
{
    if (field.IsSetLabel() &&
        field.GetLabel().IsStr() &&
        NStr::EqualNocase(field.GetLabel().GetStr(), kSuppressFieldLabel)) {
        return true;
    } else {
        return false;
    }
}
 
 
void CValidErrorFormat::AddSuppression(CUser_object& user, CValidErrItem::TErrIndex error_code)
{   
    CValidErrorSuppress::AddSuppression(user, error_code);
}
 
 
void CValidErrorFormat::SetSuppressionRules(const CUser_object& user, CValidError& errors)
{
    CValidErrorSuppress::TCodes suppressedCodes;
    CValidErrorSuppress::SetSuppressedCodes(user, suppressedCodes);
    for (auto code : suppressedCodes) {
        errors.SuppressError(code);
    }
}
 
 
void CValidErrorFormat::SetSuppressionRules(const CSeq_entry& se, CValidError& errors)
{
    CValidErrorSuppress::TCodes suppressedCodes;
    CValidErrorSuppress::SetSuppressedCodes(se, suppressedCodes);
    for (auto code : suppressedCodes) {
        errors.SuppressError(code);
    }
}
 
 
void CValidErrorFormat::SetSuppressionRules(const CSeq_entry_Handle& se, CValidError& errors)
{
    SetSuppressionRules(*(se.GetCompleteSeq_entry()), errors);
}
 
 
void CValidErrorFormat::SetSuppressionRules(const CSeq_submit& ss, CValidError& errors)
{
    CValidErrorSuppress::TCodes suppressedCodes;
    CValidErrorSuppress::SetSuppressedCodes(ss, suppressedCodes);
    for (auto code : suppressedCodes) {
        errors.SuppressError(code);
    }
}
 
 
void CValidErrorFormat::SetSuppressionRules(const CBioseq& seq, CValidError& errors)
{
    CValidErrorSuppress::TCodes suppressedCodes;
    CValidErrorSuppress::SetSuppressedCodes(seq, suppressedCodes);
    for (auto code : suppressedCodes) {
        errors.SuppressError(code);
    }
}
 
 
//LCOV_EXCL_START
//not used by asnvalidate but may be useful for other clients of validator library
void CValidErrorFormat::AddLocusTags(CValidError& errors, CScope& scope)
{
    for (auto it : errors.SetErrs()) {
        if (it->IsSetLocus_tag()) {
            continue;
        }
        if (it->IsSetObjectType() &&
            it->GetObjectType() == CValidErrItem::eObjectType_seqfeat &&
            it->IsSetObject() &&
            it->GetObject().GetThisTypeInfo() == CSeq_feat::GetTypeInfo()) {
            const CSeq_feat* sf = static_cast<const CSeq_feat *>(&(it->GetObject()));
            if (sf && sf->IsSetData()) {
                it->SetLocus_tag(x_GetLocusTag(*sf, scope));
            }
        }
    }
}
 
 
const string& CValidErrorFormat::x_GetLocusTag(const CSeq_feat& sf, CScope& scope)
{
    const string* rval = &kEmptyStr;
 
    if (sf.GetData().IsGene()) {
        if (sf.GetData().GetGene().IsSetLocus_tag()) {
            rval = &sf.GetData().GetGene().GetLocus_tag();
        }
    } else {
        const CGene_ref* g = sf.GetGeneXref();
        if (g && g->IsSetLocus_tag()) {
            rval = &g->GetLocus_tag();
        } else {
            CConstRef<CSeq_feat> gene = sequence::GetGeneForFeature(sf, scope);
            if (gene && gene->GetData().GetGene().IsSetLocus_tag()) {
                rval = &gene->GetData().GetGene().GetLocus_tag();
            }
        }
    }
    return *rval;
}
//LCOV_EXCL_STOP
 
 
END_SCOPE(validator)
END_SCOPE(objects)
END_NCBI_SCOPE