Seq_feat.cpp

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/* $Id: Seq_feat.cpp 97464 2022-07-20 12:28:40Z 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:  .......
 *
 * File Description:
 *   .......
 *
 * Remark:
 *   This code was originally generated by application DATATOOL
 *   using specifications from the ASN data definition file
 *   'seqfeat.asn'.
 */
 
// generated includes
#include <ncbi_pch.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/seq/seqport_util.hpp>
#include <vector>
 
 
BEGIN_NCBI_SCOPE
 
BEGIN_objects_SCOPE // namespace ncbi::objects::
 
 
// destructor
CSeq_feat::~CSeq_feat(void)
{
}
 
 
BEGIN_LOCAL_NAMESPACE;
 
 
static int s_TypeOrder[] = {
    3, // e_not_set = 0,
    0, // e_Gene,
    3, // e_Org,
    2, // e_Cdregion,
    3, // e_Prot,
    1, // e_Rna,
    3  // e_Pub, and the rest
};
 
 
static inline
bool s_IsOperon(const CSeqFeatData& fd)
{
    return fd.Which() == CSeqFeatData::e_Imp &&
        fd.GetSubtype() == CSeqFeatData::eSubtype_operon;
}
 
 
static inline 
int s_GetCdregionOrder(const CSeqFeatData& fd)
{
    CCdregion::EFrame frame = fd.GetCdregion().GetFrame();
    if ( frame == CCdregion::eFrame_not_set ) {
        frame = CCdregion::eFrame_one;
    }
    return frame;
}
 
 
END_LOCAL_NAMESPACE;
 
 
int CSeq_feat::GetTypeSortingOrder(CSeqFeatData::E_Choice type)
{
    return s_TypeOrder[min(size_t(type),
                           sizeof(s_TypeOrder)/sizeof(s_TypeOrder[0])-1)];
}
 
 
// Corresponds to SortFeatItemListByPos from the C toolkit
int CSeq_feat::CompareNonLocation(const CSeq_feat& f2,
                                  const CSeq_loc& loc1,
                                  const CSeq_loc& loc2) const
{
    const CSeqFeatData& data1 = GetData();
    const CSeqFeatData& data2 = f2.GetData();
    CSeqFeatData::E_Choice type1 = data1.Which();
    CSeqFeatData::E_Choice type2 = data2.Which();
 
    // operon first
    if ( int diff = s_IsOperon(data2) - s_IsOperon(data1) ) {
        return diff;
    }
    if ( type1 != type2 ) {
        // order by feature type
        int order1 = GetTypeSortingOrder(type1);
        int order2 = GetTypeSortingOrder(type2);
        int diff = order1 - order2;
        if ( diff != 0 )
            return diff;
    }
 
    // minus strand last
    ENa_strand strand1 = loc1.GetStrand();
    ENa_strand strand2 = loc2.GetStrand();
    if ( int diff = IsReverse(strand1) - IsReverse(strand2) ) {
        return diff;
    }
 
    if ( int diff = loc1.CompareSubLoc(loc2, strand1) ) {
        return diff;
    }
 
    {{ // compare subtypes
        CSeqFeatData::ESubtype subtype1 = data1.GetSubtype();
        CSeqFeatData::ESubtype subtype2 = data2.GetSubtype();
        int diff = subtype1 - subtype2;
        if ( diff != 0 )
            return diff;
    }}
 
    // subtypes are equal, types must be equal too
    _ASSERT(type1 == type2);
 
    // type dependent comparison
    if ( type1 == CSeqFeatData::e_Cdregion ) {
        // compare frames of identical CDS ranges
        if ( int diff = s_GetCdregionOrder(data1)-s_GetCdregionOrder(data2) ) {
            return diff;
        }
    }
    else if ( type1 == CSeqFeatData::e_Imp ) {
        // compare labels of imp features
        int diff = NStr::CompareNocase(data1.GetImp().GetKey(),
                                       data2.GetImp().GetKey());
        if ( diff != 0 )
            return diff;
    }
 
    // XXX - should compare parent seq-annots
    // XXX 1. parent Seq-annot idx.itemID
    // XXX 2. features itemID
 
    return 0; // unknown
}
 
 
int CSeq_feat::CompareStrict(const CSeq_feat& f2) const
{
    int diff = Compare(f2);
    if (diff) return diff;
    stringstream s1, s2;
    s1 << MSerial_AsnText << *this;
    s2 << MSerial_AsnText << f2;
    return s1.str().compare(s2.str());
}
 
 
const CGene_ref* CSeq_feat::GetGeneXref(void) const
 
{
    ITERATE(CSeq_feat::TXref, it, GetXref ()) {
        if ((*it)->IsSetData () && (*it)->GetData ().IsGene ()) {
            return &((*it)->GetData ().GetGene ());
        }
    }
    return 0;
}
 
void CSeq_feat::SetGeneXref(CGene_ref& value)
 
{
    TXref& xref = SetXref();
    NON_CONST_ITERATE(CSeq_feat::TXref, it, SetXref ()) {
        CSeqFeatXref& ref = **it;
        if (ref.IsSetData() && ref.GetData().IsGene()) {
            ref.SetData().SetGene(value);
            return;
        }
    }
    CRef<CSeqFeatXref> gref(new CSeqFeatXref);
    xref.push_back(gref);
    gref->SetData().SetGene(value);
}
 
CGene_ref& CSeq_feat::SetGeneXref(void)
{
    TXref& xref = SetXref();
    NON_CONST_ITERATE(CSeq_feat::TXref, it, xref) {
        CSeqFeatXref& ref = **it;
        if (ref.IsSetData() && ref.GetData().IsGene()) {
            return ref.SetData().SetGene();
        }
    }
    CRef<CSeqFeatXref> gref(new CSeqFeatXref);
    xref.push_back(gref);
    return gref->SetData().SetGene();
}
 
const CProt_ref* CSeq_feat::GetProtXref(void) const
 
{
    ITERATE(CSeq_feat::TXref, it, GetXref ()) {
        if ((*it)->IsSetData () && (*it)->GetData ().IsProt ()) {
            return &((*it)->GetData ().GetProt ());
        }
    }
    return 0;
}
 
void CSeq_feat::SetProtXref(CProt_ref& value)
 
{
    TXref& xref = SetXref();
    NON_CONST_ITERATE(CSeq_feat::TXref, it, xref) {
        CSeqFeatXref& ref = **it;
        if (ref.IsSetData() && ref.GetData().IsProt()) {
            ref.SetData().SetProt(value);
            return;
        }
    }
    CRef<CSeqFeatXref> pref(new CSeqFeatXref);
    xref.push_back(pref);
    pref->SetData().SetProt(value);
}
 
CProt_ref& CSeq_feat::SetProtXref(void)
 
{
    TXref& xref = SetXref();
    NON_CONST_ITERATE(CSeq_feat::TXref, it, xref) {
        CSeqFeatXref& ref = **it;
        if (ref.IsSetData() && ref.GetData().IsProt()) {
            return ref.SetData().SetProt();
        }
    }
    CRef<CSeqFeatXref> pref(new CSeqFeatXref);
    xref.push_back(pref);
    return pref->SetData().SetProt();
}
 
 
bool CSeq_feat::HasSeqFeatXref(const CSeqFeatXref::TId& id) const
{
    if (!IsSetXref()) {
        return false;
    }
    ITERATE(CSeq_feat::TXref, xit, GetXref()) {
        if ((*xit)->IsSetId() && (*xit)->GetId().Equals(id)) {
            return true;
        }
    }
    return false;
}
 
 
bool CSeq_feat::AddSeqFeatXref(const CSeqFeatXref::TId& id)
{
    if (HasSeqFeatXref(id)) {
        return false;
    }
    CRef<CSeqFeatXref> x1(new CSeqFeatXref());
    x1->SetId().Assign(id);
    SetXref().push_back(x1);
    return true;
}
 
 
void CSeq_feat::AddQualifier(const string& qual_name, const string& qual_val)
{
    CRef<CGb_qual> qual(new CGb_qual());
    qual->SetQual(qual_name);
    qual->SetVal(qual_val);
    SetQual().push_back(qual);
}
 
void CSeq_feat::AddOrReplaceQualifier(
    const string& qual_name, const string& qual_val)
{
    if (IsSetQual()) {
        NON_CONST_ITERATE (TQual, iter, SetQual()) {
            if ( (*iter)->GetQual() == qual_name ) {
                (*iter)->SetVal(qual_val);
                return;
            }
        }
    }
 
    // we didn't find an already-existing qual, so we add it
    AddQualifier(qual_name, qual_val);
}
 
void CSeq_feat::RemoveQualifier(const string& qual_name)
{
    // qual is a vector so we have to be careful; carelessly
    // removing all quals that match as we find them
    // is a potentially quadratic-time operation.
    // Instead we construct a new qual vector and do a swap (swap should
    // be a constant-time operation)
 
    if( ! IsSetQual() ) {
        return;
    }
 
    TQual new_qual_vec;
    new_qual_vec.reserve(GetQual().size());
 
    ITERATE (TQual, iter, GetQual()) {
        if ( (*iter)->GetQual() != qual_name ) {
            new_qual_vec.push_back(*iter);
        }
    }
 
    if( new_qual_vec.size() != GetQual().size() ) {
        // swap should be a constant-time operation
        if ( new_qual_vec.empty() ) {
            ResetQual();
        }
        else {
            SetQual().swap(new_qual_vec);
        }
    }
}
 
void CSeq_feat::AddDbxref(const string& db, const string& tag)
{
    CRef<CDbtag> dbtag(new CDbtag());
    dbtag->SetDb(db);
    dbtag->SetTag().SetStr(tag);
    SetDbxref().push_back(dbtag);
}
 
 
void CSeq_feat::AddDbxref(const string& db, int tag)
{
    CRef<CDbtag> dbtag(new CDbtag());
    dbtag->SetDb(db);
    dbtag->SetTag().SetId(tag);
    SetDbxref().push_back(dbtag);
}
 
void CSeq_feat::AddExceptText(const string & exception_text)
{
    // always set this
    SetExcept(true);
 
    if( ! IsSetExcept_text() ) {
        SetExcept_text(exception_text);
        return;
    }
 
    if( HasExceptionText(exception_text) ) {
        // nothing to do; it already has it
        return;
    }
 
    string & sCurrentExceptTextContents = SetExcept_text();
    if( ! sCurrentExceptTextContents.empty() ) {
        sCurrentExceptTextContents += ", ";
    }
    sCurrentExceptTextContents += NStr::TruncateSpaces(exception_text);
}
 
void CSeq_feat::RemoveExceptText(const string & exception_text)
{
    if( ! IsSetExcept() || ! GetExcept() || ! IsSetExcept_text()  ) {
        return;
    }
 
    list<CTempString> list_of_except_texts;
    NStr::Split(GetExcept_text(), ",", list_of_except_texts, NStr::fSplit_Tokenize);
 
    // remove occurrences of exception_text (case-insensitive)
    string new_except_texts; // build answer in this variable
    ITERATE(list<CTempString>, text_it, list_of_except_texts) {
        if( ! NStr::EqualNocase(*text_it, exception_text) ) {
            if( ! new_except_texts.empty() ) {
                new_except_texts += ", ";
            }
            new_except_texts += NStr::TruncateSpaces_Unsafe(*text_it);
        }
    }
 
    // no exceptions left, so erase
    if( new_except_texts.empty() ) {
        ResetExcept();
    }
 
    // swap faster than assignment
    SetExcept_text().swap(new_except_texts);
}
 
CConstRef<CDbtag> CSeq_feat::GetNamedDbxref(const CTempString& db) const
{
    if (IsSetDbxref()) {
        ITERATE (TDbxref, iter, GetDbxref()) {
            if ( (*iter)->GetDb() == db) {
                return *iter;
            }
        }
    }
 
    return CConstRef<CDbtag>();
}
 
 
const string& CSeq_feat::GetNamedQual(const CTempString& qual_name) const
{
    if (IsSetQual()) {
        ITERATE (TQual, iter, GetQual()) {
            if ( (*iter)->GetQual() == qual_name  &&  (*iter)->IsSetVal()) {
                return (*iter)->GetVal();
            }
        }
    }
 
    return kEmptyStr;
}
 
AutoPtr<CSeq_feat::TExceptionTextSet> 
CSeq_feat::GetTempExceptionTextSet(void) const
{
    AutoPtr<TExceptionTextSet> pAnswerSet( new TExceptionTextSet );
 
    if( ! IsSetExcept() || ! GetExcept() || ! IsSetExcept_text()  ) 
    {
        return pAnswerSet; // empty set
    }
 
    const string & raw_exception_texts = GetExcept_text();
 
    vector<CTempStringEx> exception_parts;
    NStr::Split(raw_exception_texts, ",", exception_parts, NStr::fSplit_Tokenize);
 
    ITERATE( vector<CTempStringEx>, part_it, exception_parts ) {
        pAnswerSet->insert( NStr::TruncateSpaces_Unsafe(*part_it) );
    }
 
    return pAnswerSet;
}
 
bool CSeq_feat::HasExceptionText(const string & exception_text ) const
{
    CTempString sCleanedInputText =
        NStr::TruncateSpaces_Unsafe(exception_text);
 
    if( sCleanedInputText.empty() ) {
        // it's preferable for the caller not to give us an
        // empty string, but... just in ycase
        return false;
    }
 
    AutoPtr<TExceptionTextSet> p_exception_text_set = GetTempExceptionTextSet();
 
    // is it in the set?
    return ( p_exception_text_set->find(sCleanedInputText) != 
        p_exception_text_set->end() );
}
 
 
// second element in pair indicates whether exception text is
// permitted only for RefSeq records
typedef SStaticPair<const char*, bool>  TExceptionPairElem;
static const TExceptionPairElem k_LegalExceptionMap[] = {
    { "16S ribosomal RNA and 23S ribosomal RNA overlap", true },
    { "16S ribosomal RNA and 5S ribosomal RNA overlap", true },
    { "23S ribosomal RNA and 16S ribosomal RNA overlap", true },
    { "23S ribosomal RNA and 5S ribosomal RNA overlap", true },
    { "5S ribosomal RNA and 16S ribosomal RNA overlap", true },
    { "5S ribosomal RNA and 23S ribosomal RNA overlap", true },
    { "adjusted for low-quality genome", true },
    { "alternative processing", false },
    { "alternative start codon", false },
    { "annotated by transcript or proteomic data", false },
    { "artificial frameshift", false },
    { "artificial location", false },
    { "circular RNA", false },
    { "dicistronic gene", false },
    { "gene split at contig boundary", false },
    { "gene split at sequence boundary", false },
    { "genetic code exception", false },
    { "heterogeneous population sequenced", false },
    { "low-quality sequence region", false },
    { "mismatches in transcription", true },
    { "mismatches in translation", true },
    { "modified codon recognition", false },
    { "nonconsensus splice site", false },
    { "rearrangement required for product", false },
    { "reasons given in citation", false },
    { "ribosomal slippage", false },
    { "RNA editing", false },
    { "trans-splicing", false },
    { "transcribed product replaced", false },
    { "transcribed pseudogene", false },
    { "translated product replaced", false },
    { "translation initiation by tRNA-Leu at CUG codon", true },
    { "unclassified transcription discrepancy", true },
    { "unclassified translation discrepancy", true },
    { "unextendable partial coding region", false }
};
typedef CStaticArrayMap<const char*, bool, PNocase_CStr> TExceptionPairMap;
DEFINE_STATIC_ARRAY_MAP(TExceptionPairMap, sc_ExceptionPairMap, k_LegalExceptionMap);
 
vector<string> CSeq_feat::GetListOfLegalExceptions(bool include_refseq)
{
    vector<string> exception_list;
 
    TExceptionPairMap::const_iterator it = sc_ExceptionPairMap.begin();
    while (it != sc_ExceptionPairMap.end()) {
        if (include_refseq || !it->second) {
            exception_list.push_back(it->first);
        }
        ++it;
    }
 
    return exception_list;
}
 
 
bool CSeq_feat::IsExceptionTextInLegalList(const string& exception_text, bool allow_refseq)
{
    TExceptionPairMap::const_iterator it = sc_ExceptionPairMap.find(exception_text.c_str());
    if (it != sc_ExceptionPairMap.end() && (allow_refseq || !it->second)) {
        return true;
    } else {
        return false;
    }
}
 
 
bool CSeq_feat::IsExceptionTextRefSeqOnly(const string& exception_text)
{
    TExceptionPairMap::const_iterator it = sc_ExceptionPairMap.find(exception_text.c_str());
    if (it == sc_ExceptionPairMap.end()) {
        return false;
    } else {
        return it->second;
    }
}
 
 
CConstRef<CUser_object> CSeq_feat::FindExt(const string& ext_type) const
{
    CConstRef<CUser_object> ret;
    if ( IsSetExts() ) {
        ITERATE(TExts, it, GetExts()) {
            const CObject_id& obj_type = (*it)->GetType();
            if ( obj_type.IsStr()  &&  obj_type.GetStr() == ext_type ) {
                ret.Reset(it->GetPointer());
                break;
            }
        }
    }
    if ( !ret  &&  IsSetExt()) {
        if (GetExt().GetType().IsStr()) {
            if (GetExt().GetType().GetStr() == ext_type) {
                ret.Reset(&GetExt());
            }
            else if (GetExt().GetType().GetStr() == "CombinedFeatureUserObjects") {
                ITERATE (TExt::TData, it, GetExt().GetData()) {
                    const CUser_field& f = **it;
                    if (f.GetData().IsObject()  &&
                        f.GetData().GetObject().GetType().IsStr()  &&
                        f.GetData().GetObject().GetType().GetStr()  == ext_type) {
                        ret.Reset(&f.GetData().GetObject());
                        break;
                    }
                }
            }
        }
    }
    return ret;
}
 
CRef<CUser_object> CSeq_feat::FindExt(const string& ext_type)
{
    CRef<CUser_object> ret;
    if ( IsSetExts() ) {
        NON_CONST_ITERATE(TExts, it, SetExts()) {
            const CObject_id& obj_type = (*it)->GetType();
            if ( obj_type.IsStr()  &&  obj_type.GetStr() == ext_type ) {
                ret.Reset(it->GetPointer());
                break;
            }
        }
    }
    if ( !ret  &&  IsSetExt()) {
        if (GetExt().GetType().IsStr()) {
            if (GetExt().GetType().GetStr() == ext_type) {
                ret.Reset(&SetExt());
            }
            else if (GetExt().GetType().GetStr() == "CombinedFeatureUserObjects") {
                NON_CONST_ITERATE (TExt::TData, it, SetExt().SetData()) {
                    CUser_field& f = **it;
                    if (f.GetData().IsObject()  &&
                        f.GetData().GetObject().GetType().IsStr()  &&
                        f.GetData().GetObject().GetType().GetStr()  == ext_type) {
                        ret.Reset(&f.SetData().SetObject());
                        break;
                    }
                }
            }
        }
    }
    return ret;
}
 
void
CSeq_feat::AddExt(CRef<CUser_object> ext, TAddExt add_flags)
{
    // ext must have type set
    if( ! ext->IsSetType() || ! ext->GetType().IsStr()) {
        NCBI_USER_THROW("Seq-feat Ext must have a type");
    }
 
    // if requested, remove all previous ones, effectively simulating
    // a replace function.
    if( add_flags & fAddExt_ReplaceAll ) {
        const string & ext_type = ext->GetType().GetStr();
        RemoveExt(ext_type);
    }
 
    SetExts().push_back(ext);
}
 
void
CSeq_feat::RemoveExt(const string& ext_type)
{
    if ( IsSetExts() ) {
        TExts & exts = SetExts();
        // Exts are list, so constant time removal per element
        ERASE_ITERATE(TExts, it, exts) {
            const CObject_id& obj_type = (*it)->GetType();
            if ( obj_type.IsStr()  &&  obj_type.GetStr() == ext_type ) {
                exts.erase(it);
            }
        }
        if( exts.empty() ) {
            ResetExts();
        }
    }
    if ( IsSetExt()) {
        if (GetExt().GetType().IsStr()) {
            if (GetExt().GetType().GetStr() == ext_type) {
                ResetExt();
            }
            else if (GetExt().GetType().GetStr() == "CombinedFeatureUserObjects") {
                // build new ext vector since cannot remove easily as
                // we go along.
                TExt::TData new_ext_data;
                TExt::TData & curr_ext_data = SetExt().SetData();
                NON_CONST_ITERATE (TExt::TData, it, curr_ext_data) {
                    CUser_field& f = **it;
                    if (f.GetData().IsObject()  &&
                        f.GetData().GetObject().GetType().IsStr()  &&
                        f.GetData().GetObject().GetType().GetStr()  == ext_type) {
                        continue;
                    }
                    new_ext_data.push_back(*it);
                }
 
                if( new_ext_data.empty() ) {
                    ResetExt();
                } else if( new_ext_data.size() != curr_ext_data.size() ) {
                    // swap is constant time
                    new_ext_data.swap(curr_ext_data);
                }
            }
        }
    }
}
 
 
ISeq_feat::~ISeq_feat(void)
{
}
 
END_objects_SCOPE // namespace ncbi::objects::
 
END_NCBI_SCOPE
 
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