OrgName.cpp

Go to the documentation of this file.

Go to the SVN repository for this file.

/* $Id: OrgName.cpp 79377 2017-09-06 15:45:28Z domrach $
 * ===========================================================================
 *
 *                            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 data definition file
 *   'seqfeat.asn'.
 */
 
// standard includes
 
// generated includes
#include <ncbi_pch.hpp>
#include <objects/seqfeat/OrgName.hpp>
 
#include <objects/seqfeat/PartialOrgName.hpp>
#include <objects/seqfeat/TaxElement.hpp>
 
// generated classes
 
BEGIN_NCBI_SCOPE
 
BEGIN_objects_SCOPE // namespace ncbi::objects::
 
// destructor
COrgName::~COrgName(void)
{
}
 
 
bool COrgName::GetFlatName(string& name_out, string* lineage) const
{
    if (lineage  &&  lineage->empty()  &&  IsSetLineage()) {
        *lineage = GetLineage();
    }
    
    if ( !IsSetName() ) {
        return false;
    }
 
    const TName& name = GetName();
    name_out.clear();
    switch (name.Which()) {
    case C_Name::e_Namedhybrid: {
    const CBinomialOrgName& bin = name.GetNamedhybrid();
    name_out += bin.GetGenus();
    if( bin.IsSetSpecies() ) {
        name_out += " x ";
        name_out += bin.GetSpecies();
    }
    return true;
    }
    case C_Name::e_Binomial:  {
        const CBinomialOrgName& bin = name.GetBinomial();
        if (bin.IsSetSpecies()) {
        string sSpecies = bin.GetSpecies();
        if( sSpecies.find(" ") != string::npos &&
        !( NStr::StartsWith(sSpecies,"sp. ") ||
           NStr::StartsWith(sSpecies,"species ") ) ) {
        // When species epithet is complex -- occurs when genus name doesn't coincide with beginning of species name
        name_out += sSpecies;
        } else { // Simple case with single genus and species epithets
        if (bin.IsSetSubspecies() && !NStr::TruncateSpaces(bin.GetSubspecies()).empty()) {
            string sSubspecies = NStr::TruncateSpaces(bin.GetSubspecies());
            bool bSubspIndicator = NStr::StartsWith(sSubspecies, "subsp. ") ||
            NStr::StartsWith(sSubspecies, "ssp. ") ||
            NStr::StartsWith(sSubspecies, "subspecies ");
            if( sSubspecies.find(" ") != string::npos && !bSubspIndicator ) { 
            // When subspecies epithet is complex -- occurs when species name doesn't coincide with beginning of subspecies name
            name_out += sSubspecies;
            } else { // Simple case with single sub-species epithet
            name_out += bin.GetGenus();
            name_out += ' ' + bin.GetSpecies();
            if( !bSubspIndicator ) {
                string sNomenclature;
                bool bZooCode = false;
                if( GetNomenclature( sNomenclature ) ) {
                bZooCode = sNomenclature == "Z";
                } else { // we still have to support old nomenclature-less orgnames
                string sLineage = lineage ? *lineage : IsSetLineage() ? GetLineage() : NcbiEmptyString;
                bZooCode = sLineage.find("Metazoa;") != string::npos ||
                    sLineage.find("Slopalinida;") != string::npos ||
                    sLineage.find("Blastocystis;") != string::npos;
                }
                if( !bZooCode ) {
                name_out += " subsp.";
                } else { // check if subspecies is well-specified
                if( sSubspecies.find_first_not_of("abcdefghijklmnopqrstuvwxyz-") != string::npos ||
                    sSubspecies[0] == '-' ) {
                    name_out += " ssp.";
                }
                }
            }
            name_out += ' ' + sSubspecies;
            }
        } else { // No subspecies
            name_out += bin.GetGenus();
            name_out += ' ' + bin.GetSpecies();
        }
        if( IsSetMod() ) { // Add variety and forma to flat name -- those are valid classification categories
            ITERATE (COrgName::TMod, it, GetMod()) {
            if( (*it)->GetSubtype() == COrgMod::eSubtype_variety ) {
                name_out += " var. ";
                name_out += (*it)->GetSubname();
                break;
            }
            }
            ITERATE (COrgName::TMod, it, GetMod()) {
            if( (*it)->GetSubtype() == COrgMod::eSubtype_forma ) {
                name_out += " f. ";
                name_out += (*it)->GetSubname();
                break;
            } else if( (*it)->GetSubtype() == COrgMod::eSubtype_forma_specialis ) {
                name_out += " f.sp. ";
                name_out += (*it)->GetSubname();
                break;
            }
            }
        }
        }
        }
        return true;
    }
 
    case COrgName::C_Name::e_Virus:
        name_out = name.GetVirus();
        return true;
 
    case COrgName::C_Name::e_Hybrid:
    {
    string tmp;
    string delim;
    string sLineage = lineage ? *lineage : IsSetLineage() ? GetLineage() : NcbiEmptyString;
        ITERATE (CMultiOrgName::Tdata, it, name.GetHybrid().Get()) {
        tmp.clear();
            if ((*it)->GetFlatName(tmp, &sLineage)) {
        name_out += delim;
        if( (*it)->IsSetName() && (*it)->GetName().IsHybrid() ) {
            name_out += '(';
            name_out += tmp;
            name_out += ')';
        } else {
            name_out += tmp;
        }
        delim = " x ";
            } else {
        return false;
        }
        }
    return true;
    }
 
    case COrgName::C_Name::e_Partial:
    {
        string delim;
        ITERATE (CPartialOrgName::Tdata, it, name.GetPartial().Get()) {
            name_out += delim + (*it)->GetName();
            delim = " ";
        }
        return true;
    }
    
    default:
        return false;
    }
}
 
// The proposed format for orgname flags: flagname1[;flagname2]...[;flagnameN]
// where flagnameX consists of ascii alphanum characters only. Each value of flagnameX is unique.
// Presence of flag name in the strings means 'true' value for the flag.
const CTempString s_flagDelim = ";";
 
void COrgName::x_SetAttribFlag( const string& name, bool bStartsWith )
{
    if( !x_GetAttribFlag( name, bStartsWith ) ) {
    if( IsSetAttrib() && !GetAttrib().empty() ) {
        SetAttrib().append(s_flagDelim).append(name);
    } else {
        SetAttrib( name );
    }
    }
}
 
void COrgName::x_ResetAttribFlag( const string& name, bool bStartsWith )
{
    if( !name.empty() && IsSetAttrib() ) {
        const string& attr = GetAttrib();
        list< CTempString > lVals;
        NStr::Split(attr, s_flagDelim, lVals, NStr::fSplit_Tokenize);
        for( list< CTempString >::iterator i = lVals.begin(), li = lVals.end(); i != li; ) {
            NStr::TruncateSpacesInPlace( *i );
            if( (!bStartsWith && NStr::EqualNocase( *i, name )) ||
        (bStartsWith && NStr::StartsWith( *i, name, NStr::eNocase )) ) {
                i = lVals.erase( i );
            } else {
                ++i;
            }
        }
        SetAttrib( NStr::Join( lVals, s_flagDelim ) );
        if( SetAttrib().empty() ) {
            ResetAttrib();
        }
    }
}
 
bool COrgName::x_GetAttribFlag( const string& name, bool bStartsWith ) const
{
    if( !name.empty() && IsSetAttrib() ) {
    const string& attr = GetAttrib();
    list< CTempString > lVals;
    NStr::Split(attr, s_flagDelim, lVals, NStr::fSplit_Tokenize);
    NON_CONST_ITERATE( list< CTempString >, i, lVals ) {
        NStr::TruncateSpacesInPlace( *i );
        if( (!bStartsWith && NStr::EqualNocase( *i, name )) ||
        (bStartsWith && NStr::StartsWith( *i, name, NStr::eNocase )) ) {
        return true;
        }
    }
    }
    return false;
}
 
// Getting attribute value for pairs like attrname=value;
// value cannot contain ';'
bool COrgName::x_GetAttribValue( const string& name, string& sValue ) const
{
    if( !name.empty() && IsSetAttrib() ) {
    const string& attr = GetAttrib();
    list< CTempString > lVals;
    NStr::Split(attr, s_flagDelim, lVals, NStr::fSplit_Tokenize);
    NON_CONST_ITERATE( list< CTempString >, i, lVals ) {
        NStr::TruncateSpacesInPlace( *i );
        if( NStr::StartsWith( *i, name, NStr::eNocase ) &&
        i->size() > name.size() && (*i)[name.size()] == '=' ) {
        sValue.assign( i->substr(name.size()+1) );
        return true;
        }
    }
    }
    return false;
}
 
// Flag indicating that node's scientific name is "well specified" according to the
// respective taxonomic nomenclature (e.g. Genus species subspecies). 
// Based on "specified" property from Taxonomy database
bool COrgName::IsFormalName() const
{
    return x_GetAttribFlag( "specified" );
}
 
void COrgName::SetFormalNameFlag( bool bFormalName )
{
    if( bFormalName ) {
    x_SetAttribFlag( "specified" );
    } else {
    x_ResetAttribFlag( "specified" );
    }
}
 
bool COrgName::IsUncultured() const
{
    return x_GetAttribFlag( "uncultured" );
}
 
void COrgName::SetUncultured( bool bUncultured )
{
    if( bUncultured ) {
        x_SetAttribFlag( "uncultured" );
    } else {
        x_ResetAttribFlag( "uncultured" );
    }
}
 
// Modifier forwarding flag. Used during org-ref lookup to enable/disable
// modifier forwarding. If set modifier forwarding is disabled.
// Flag is kept along with other flags in orgname.attrib field
// (see comments to x_SetAttribFlag() function)
bool COrgName::IsModifierForwardingDisabled() const
{
    return x_GetAttribFlag( "nomodforward" );
}
 
void COrgName::DisableModifierForwarding()
{
    x_SetAttribFlag( "nomodforward" );
}
 
void COrgName::EnableModifierForwarding()
{
    x_ResetAttribFlag( "nomodforward" );
}
 
#define MAKE_COMMON(o1,o2,o3,Field) if (o1.IsSet##Field() && o2.IsSet##Field() && NStr::Equal(o1.Get##Field(), o2.Get##Field())) o3.Set##Field(o1.Get##Field());
#define MAKE_COMMON_INT(o1,o2,o3,Field) if (o1.IsSet##Field() && o2.IsSet##Field() && o1.Get##Field() == o2.Get##Field()) o3.Set##Field(o1.Get##Field());
 
CRef<COrgName> COrgName::MakeCommon(const COrgName& other) const
{
    bool any = false;
    CRef<COrgName> common(new COrgName());
 
    // name
    if (IsSetName() && other.IsSetName() && GetName().Equals(other.GetName())) {
        common->SetName().Assign(GetName());
        any = true;
    }
 
    // mod
    if (IsSetMod() && other.IsSetMod()) {
        ITERATE(TMod, it1, GetMod()) {
            bool found = false;
            ITERATE(TMod, it2, other.GetMod()) {
                if ((*it1)->Equals(**it2)) {
                    found = true;
                }
            }
            if (found) {
                CRef<COrgMod> add(new COrgMod());
                add->Assign(**it1);
                common->SetMod().push_back(add);
                any = true;
            }
        }
    }
 
    MAKE_COMMON((*this), other, (*common), Attrib);
    MAKE_COMMON((*this), other, (*common), Lineage);
    MAKE_COMMON((*this), other, (*common), Div);
    MAKE_COMMON_INT((*this), other, (*common), Gcode);
    MAKE_COMMON_INT((*this), other, (*common), Mgcode);
    MAKE_COMMON_INT((*this), other, (*common), Pgcode);
    if (common->IsSetAttrib() || common->IsSetLineage() || common->IsSetDiv() ||
        common->IsSetGcode() || common->IsSetMgcode() || common->IsSetPgcode()) {
        any = true;
    }
 
    if (!any) {
        common.Reset(NULL);
    }
    return common;
}
 
// Nomenclature information stored in attrib field as string in following format:
// nomenclature=[BPVZ]*;
bool COrgName::GetNomenclature( string& result ) const
{
    if( IsSetMod() ) {
        ITERATE( COrgName::TMod, ci, GetMod() ) {
            if( (*ci)->GetSubtype() == COrgMod::eSubtype_nomenclature ) {
                result = (*ci)->GetSubname();
                return true;
            }
        }
    }
    return false;
}
 
// returns false if value is unsupported
bool COrgName::SetNomenclature( const string& nomenclature )
{
    // Analyze value. Make sure it consists of [BPVZ]
    char norm_nom[4];
    memset( norm_nom, 0, sizeof(norm_nom) );
    ITERATE( string, ci, nomenclature ) {
    switch( *ci ) {
    case 'b': case 'B': norm_nom[0] = 'B'; break;
    case 'p': case 'P': norm_nom[1] = 'P'; break;
    case 'v': case 'V': norm_nom[2] = 'V'; break;
    case 'z': case 'Z': norm_nom[3] = 'Z'; break;
    default: return false;
    }
    }
    string sNewVal;
    for( size_t i = 0; i < sizeof(norm_nom); ++i ) {
    if( norm_nom[i] != 0 ) {
        sNewVal += norm_nom[i];
    }
    }
    
    string sOldVal;
    if( GetNomenclature( sOldVal ) ) {
    if( sOldVal == sNewVal ) {
        return true; // already set to this value
    } else {
        ResetNomenclature();
    }
    }
    if( !sNewVal.empty() ) {
        CRef<COrgMod> pMod( new COrgMod( COrgMod::eSubtype_nomenclature, sNewVal ) );
        SetMod().push_back( pMod );
    }
    return true;
}
 
// returns false if value is unsupported
void COrgName::ResetNomenclature()
{
    RemoveModBySubtype( COrgMod::eSubtype_nomenclature );
}
 
unsigned int // returns number of removed modifiers
COrgName::RemoveModBySubtype( COrgMod::ESubtype to_remove )
{
    unsigned result = 0;
    if( IsSetMod() ) {
    for( TMod::iterator i = SetMod().begin(); i != SetMod().end(); ) {
        if( (*i)->GetSubtype() == to_remove ) {
        i = SetMod().erase(i);
        ++result;
        } else {
        ++i;
        }
    }
    }
    return result;
}
 
END_objects_SCOPE // namespace ncbi::objects::
 
END_NCBI_SCOPE
 
/* Original file checksum: lines: 64, chars: 1877, CRC32: 38972243 */