autodef_options.cpp

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/*  $Id: autodef_options.cpp 100148 2023-06-23 19:49:35Z kans $
* ===========================================================================
*
*                            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:  Colleen Bollin
*
* File Description:
*   Generate unique definition lines for a set of sequences using organism
*   descriptions and feature clauses.
*/
 
#include <ncbi_pch.hpp>
#include <objmgr/util/autodef_options.hpp>
#include <corelib/ncbimisc.hpp>
 
#include <objects/seqfeat/BioSource.hpp>
 
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
 
            
CAutoDefOptions::CAutoDefOptions()
{
    x_Reset();
}
 
 
CRef<CUser_object> CAutoDefOptions::MakeUserObject() const
{
    CRef<CUser_object> user(new CUser_object());
 
    user->SetObjectType(CUser_object::eObjectType_AutodefOptions);
    user->SetClass("1.0");
 
    for (unsigned int i = 0; i < eOptionFieldMax; i++) {
        if (x_IsBoolean(i) && m_BooleanFlags[i]) {
            CRef<CUser_field> field = x_MakeBooleanField(i);
            user->SetData().push_back(field);
        }
    }
 
    user->SetData().push_back(x_MakeMaxMods());
    user->SetData().push_back(x_MakeFeatureListType());
    user->SetData().push_back(x_MakeMiscFeatRule());
    user->SetData().push_back(x_MakeHIVRule());
    if (!GetSpecifyNuclearProduct()) {
        user->SetData().push_back(x_MakeProductFlag());
        user->SetData().push_back(x_MakeNuclearCopyFlag());
    }
    x_MakeSuppressedFeatures(*user);
    x_MakeModifierList(*user);
    if (!NStr::IsBlank(m_TargetedLocusName)) {
        user->SetData().push_back(x_MakeTargetedLocusName());
    }
    if (!NStr::IsBlank(m_CustomFeatureClause)) {
        user->SetData().push_back(x_MakeCustomFeatureClause());
    }
 
    return user;
}
 
 
#define INITENUMFIELD(Fieldname) \
    } else if (field_type == eOptionFieldType_##Fieldname) { \
        if ((*it)->IsSetData() && (*it)->GetData().IsStr()) { \
            m_##Fieldname = Get##Fieldname((*it)->GetData().GetStr()); \
        }
 
 
void CAutoDefOptions::InitFromUserObject(const CUser_object& obj)
{
    x_Reset();
    m_BooleanFlags[eOptionFieldType_SpecifyNuclearProduct] = false;
    ITERATE(CUser_object::TData, it, obj.GetData()) {
        if ((*it)->IsSetLabel() && (*it)->GetLabel().IsStr()) {}
        TFieldType field_type = GetFieldType((*it)->GetLabel().GetStr());
        if (field_type == eOptionFieldType_Unknown && NStr::EqualNocase((*it)->GetLabel().GetStr(), "KeepPromoters")) {
            field_type = eOptionFieldType_KeepRegulatoryFeatures;
        }
        if (field_type != eOptionFieldType_Unknown) {
            if (x_IsBoolean(field_type)) {
                if ((*it)->IsSetData() && (*it)->GetData().IsBool() && (*it)->GetData().GetBool()) {
                    m_BooleanFlags[field_type] = true;
                }
            } else if (field_type == eOptionFieldType_SpecifyNuclearProduct &&
                       (*it)->GetData().IsBool() && (*it)->GetData().GetBool()) {
                m_BooleanFlags[eOptionFieldType_SpecifyNuclearProduct] = true;
            } else if (field_type == eOptionFieldType_ProductFlag) {
                if ((*it)->IsSetData() && (*it)->GetData().IsStr()) { 
                    m_ProductFlag = GetProductFlag((*it)->GetData().GetStr());
                    m_NuclearCopyFlag = CBioSource::eGenome_unknown;
                    m_BooleanFlags[eOptionFieldType_SpecifyNuclearProduct] = false;
                }
            } else if (field_type == eOptionFieldType_NuclearCopyFlag) {
                if ((*it)->IsSetData() && (*it)->GetData().IsStr()) {
                    m_NuclearCopyFlag = GetProductFlag((*it)->GetData().GetStr());
                    m_ProductFlag = CBioSource::eGenome_unknown;
                    m_BooleanFlags[eOptionFieldType_SpecifyNuclearProduct] = false;
                }
            INITENUMFIELD(FeatureListType)
            INITENUMFIELD(MiscFeatRule)
            INITENUMFIELD(HIVRule)
            }
            else if (field_type == eOptionFieldType_SuppressedFeatures) {
                x_SetSuppressedFeatures(**it);
            } else if (field_type == eOptionFieldType_MaxMods) {
                if ((*it)->IsSetData() && (*it)->GetData().IsInt()) {
                    m_MaxMods = (*it)->GetData().GetInt();
                }
            } else if (field_type == eOptionFieldType_ModifierList) {
                x_SetModifierList(**it);
            } else if (field_type == eOptionFieldType_TargetedLocusName) {
                if ((*it)->IsSetData() && (*it)->GetData().IsStr()) {
                    m_TargetedLocusName = (*it)->GetString();
                }
            } else if (field_type == eOptionFieldType_CustomFeatureClause) {
                if ((*it)->IsSetData() && (*it)->GetData().IsStr()) {
                    m_CustomFeatureClause = (*it)->GetString();
                }
            }
        }
    }
}
 
 
void CAutoDefOptions::x_Reset()
{
    m_FeatureListType = eListAllFeatures;
    m_MiscFeatRule = eNoncodingProductFeat;
    m_ProductFlag = CBioSource::eGenome_unknown;
    m_NuclearCopyFlag = CBioSource::eGenome_unknown;
    m_HIVRule = eWantBoth;
    m_MaxMods = -99;
 
    ClearSuppressedFeatures();
    ClearModifierList();
 
    for (unsigned int i = 0; i < eOptionFieldMax; i++) {
        m_BooleanFlags[i] = false;
    }
    m_BooleanFlags[eOptionFieldType_SpecifyNuclearProduct] = true;
}
 
 
typedef SStaticPair<const char *, unsigned int> TNameValPair;
const TNameValPair sc_FieldTypes[] = {
        { "AllowModAtEndOfTaxname", CAutoDefOptions::eOptionFieldType_AllowModAtEndOfTaxname },
        { "AltSpliceFlag", CAutoDefOptions::eOptionFieldType_AltSpliceFlag },
        { "CustomFeatureClause", CAutoDefOptions::eOptionFieldType_CustomFeatureClause },
        { "DoNotApplyToAff", CAutoDefOptions::eOptionFieldType_DoNotApplyToAff },
        { "DoNotApplyToCf", CAutoDefOptions::eOptionFieldType_DoNotApplyToCf },
        { "DoNotApplyToNr", CAutoDefOptions::eOptionFieldType_DoNotApplyToNr },
        { "DoNotApplyToSp", CAutoDefOptions::eOptionFieldType_DoNotApplyToSp },
        { "FeatureListType", CAutoDefOptions::eOptionFieldType_FeatureListType },
        { "GeneClusterOppStrand", CAutoDefOptions::eOptionFieldType_GeneClusterOppStrand },
        { "HIVRule", CAutoDefOptions::eOptionFieldType_HIVRule },
        { "IncludeCountryText", CAutoDefOptions::eOptionFieldType_IncludeCountryText },
        { "Keep3UTRs", CAutoDefOptions::eOptionFieldType_Keep3UTRs },
        { "Keep5UTRs", CAutoDefOptions::eOptionFieldType_Keep5UTRs },
        { "KeepAfterSemicolon", CAutoDefOptions::eOptionFieldType_KeepAfterSemicolon },
        { "KeepExons", CAutoDefOptions::eOptionFieldType_KeepExons },
        { "KeepIntrons", CAutoDefOptions::eOptionFieldType_KeepIntrons },
        { "KeepLTRs", CAutoDefOptions::eOptionFieldType_KeepLTRs },
        { "KeepMiscRecomb", CAutoDefOptions::eOptionFieldType_KeepMiscRecomb },
        { "KeepMobileElements", CAutoDefOptions::eOptionFieldType_KeepMobileElements },
        { "KeepPrecursorRNA", CAutoDefOptions::eOptionFieldType_KeepPrecursorRNA },
        { "KeepRegulatoryFeatures", CAutoDefOptions::eOptionFieldType_KeepRegulatoryFeatures },
        { "KeepRepeatRegion", CAutoDefOptions::eOptionFieldType_KeepRepeatRegion },
        { "KeepuORFs", CAutoDefOptions::eOptionFieldType_KeepuORFs },
        { "LeaveParenthetical", CAutoDefOptions::eOptionFieldType_LeaveParenthetical },
        { "MaxMods", CAutoDefOptions::eOptionFieldType_MaxMods },
        { "MiscFeatRule", CAutoDefOptions::eOptionFieldType_MiscFeatRule },
        { "ModifierList", CAutoDefOptions::eOptionFieldType_ModifierList },
        { "NuclearCopyFlag", CAutoDefOptions::eOptionFieldType_NuclearCopyFlag },
        { "ProductFlag", CAutoDefOptions::eOptionFieldType_ProductFlag },
        { "SpecifyNuclearProduct", CAutoDefOptions::eOptionFieldType_SpecifyNuclearProduct },
        { "SuppressAlleles", CAutoDefOptions::eOptionFieldType_SuppressAlleles },
        { "SuppressedFeatures", CAutoDefOptions::eOptionFieldType_SuppressedFeatures },
        { "SuppressFeatureAltSplice", CAutoDefOptions::eOptionFieldType_SuppressFeatureAltSplice },
        { "SuppressLocusTags", CAutoDefOptions::eOptionFieldType_SuppressLocusTags },
        { "SuppressMiscFeatureSubfeatures", CAutoDefOptions::eOptionFieldType_SuppressMiscFeatureSubfeatures },
        { "SuppressMobileElementSubfeatures", CAutoDefOptions::eOptionFieldType_SuppressMobileElementSubfeatures },
        { "Targeted Locus Name", CAutoDefOptions::eOptionFieldType_TargetedLocusName },
        { "UseFakePromoters", CAutoDefOptions::eOptionFieldType_UseFakePromoters },
        { "UseLabels", CAutoDefOptions::eOptionFieldType_UseLabels },
        { "UseNcRNAComment", CAutoDefOptions::eOptionFieldType_UseNcRNAComment }
};
 
typedef CStaticArrayMap<const char *, unsigned int, PNocase> TNameValPairMap;
DEFINE_STATIC_ARRAY_MAP_WITH_COPY(TNameValPairMap, sc_FieldTypeStrsMap, sc_FieldTypes);
 
const TNameValPair sc_FeatureListTypeStr[] = {
        { "Complete Genome", CAutoDefOptions::eCompleteGenome },
        { "Complete Sequence", CAutoDefOptions::eCompleteSequence },
        { "List All Features", CAutoDefOptions::eListAllFeatures },
        { "Partial Genome", CAutoDefOptions::ePartialGenome },
        { "Partial Sequence", CAutoDefOptions::ePartialSequence },
        { "Sequence", CAutoDefOptions::eSequence },
        { "Whole Genome Shotgun Sequence", CAutoDefOptions::eWholeGenomeShotgunSequence }
};
DEFINE_STATIC_ARRAY_MAP_WITH_COPY(TNameValPairMap, sc_FeatureListTypeStrsMap, sc_FeatureListTypeStr);
 
const TNameValPair sc_MiscFeatRuleStr[] = {
        { "CommentFeat", CAutoDefOptions::eCommentFeat },
        { "Delete", CAutoDefOptions::eDelete },
        { "NoncodingProductFeat", CAutoDefOptions::eNoncodingProductFeat }
};
DEFINE_STATIC_ARRAY_MAP_WITH_COPY(TNameValPairMap, sc_MiscFeatRuleStrsMap, sc_MiscFeatRuleStr);
 
const TNameValPair sc_HIVRuleStr[] = {
        { "PreferClone", CAutoDefOptions::ePreferClone },
        { "PreferIsolate", CAutoDefOptions::ePreferIsolate },
        { "WantBoth", CAutoDefOptions::eWantBoth }
};
DEFINE_STATIC_ARRAY_MAP_WITH_COPY(TNameValPairMap, sc_HIVRuleStrsMap, sc_HIVRuleStr);
 
 
 
#define AUTODEFGETENUM(Fieldname, Map, Default) \
string CAutoDefOptions::Get##Fieldname(unsigned int value) const \
{ \
    TNameValPairMap::const_iterator it = Map.begin(); \
        while (it != Map.end()) { \
        if (value == it->second) { \
            return it->first; \
        } \
        ++it; \
    } \
    return kEmptyStr; \
} \
CAutoDefOptions::T##Fieldname CAutoDefOptions::Get##Fieldname(const string& value) const \
{ \
    TNameValPairMap::const_iterator it = Map.find(value.c_str()); \
    if (it != Map.end()) { \
        return it->second; \
        } \
    return Default; \
}
 
AUTODEFGETENUM(FieldType, sc_FieldTypeStrsMap, eOptionFieldType_Unknown)
AUTODEFGETENUM(FeatureListType, sc_FeatureListTypeStrsMap, eListAllFeatures)
AUTODEFGETENUM(MiscFeatRule, sc_MiscFeatRuleStrsMap, eNoncodingProductFeat);
AUTODEFGETENUM(HIVRule, sc_HIVRuleStrsMap, eWantBoth);
 
string CAutoDefOptions::GetProductFlag(CBioSource::TGenome value) const
{
    return CBioSource::GetOrganelleByGenome(value);
}
 
 
CBioSource::TGenome CAutoDefOptions::GetProductFlag(const string& value) const
{
    return CBioSource::GetGenomeByOrganelle(value);
}
 
 
string CAutoDefOptions::GetNuclearCopyFlag(CBioSource::TGenome value) const
{
    return CBioSource::GetOrganelleByGenome(value);
}
 
 
CBioSource::TGenome CAutoDefOptions::GetNuclearCopyFlag(const string& value) const
{
    return CBioSource::GetGenomeByOrganelle(value);
}
 
 
 
bool CAutoDefOptions::x_IsBoolean(TFieldType field_type) const
{
    bool rval = true;
    switch (field_type)
    {
        case eOptionFieldType_HIVRule:
        case eOptionFieldType_FeatureListType:
        case eOptionFieldType_MiscFeatRule:
        case eOptionFieldType_ProductFlag:
        case eOptionFieldType_NuclearCopyFlag:
        case eOptionFieldType_SuppressedFeatures:
        case eOptionFieldType_ModifierList:
        case eOptionFieldType_MaxMods:
        case eOptionFieldType_TargetedLocusName:
        case eOptionFieldType_CustomFeatureClause:
            rval = false;
            break;
        default:
            rval = true;
            break;
    }
    return rval;
}
 
 
CRef<CUser_field> CAutoDefOptions::x_MakeBooleanField(TFieldType field_type) const
{
    CRef<CUser_field> field(new CUser_field());
    field->SetLabel().SetStr(GetFieldType(field_type));
    field->SetData().SetBool(true);
    return field;
}
 
 
void CAutoDefOptions::SuppressAllFeatures()
{
    ClearSuppressedFeatures();
    m_SuppressedFeatureSubtypes.push_back(CSeqFeatData::eSubtype_any);
}
 
 
bool CAutoDefOptions::IsFeatureSuppressed(CSeqFeatData::ESubtype subtype) const
{
    ITERATE(TSuppressedFeatureSubtypes, it, m_SuppressedFeatureSubtypes) {
        if (subtype == *it || *it == CSeqFeatData::eSubtype_any) {
            return true;
        }
    }
    return false;
}
 
void CAutoDefOptions::SuppressFeature(CSeqFeatData::ESubtype subtype)
{
    m_SuppressedFeatureSubtypes.push_back(subtype);
}
 
 
void CAutoDefOptions::ClearSuppressedFeatures()
{
    m_SuppressedFeatureSubtypes.clear();
}
 
 
void CAutoDefOptions::x_MakeSuppressedFeatures(CUser_object& user) const
{
    if (m_SuppressedFeatureSubtypes.empty()) {
        return;
    }
    CRef<CUser_field> field(new CUser_field());
    field->SetLabel().SetStr(GetFieldType(eOptionFieldType_SuppressedFeatures));
 
    ITERATE(TSuppressedFeatureSubtypes, it, m_SuppressedFeatureSubtypes) {
        if (*it == CSeqFeatData::eSubtype_any) {
            field->SetData().SetStr("All");
            user.SetData().push_back(field);
            return;
        }
        field->SetData().SetStrs().push_back(CSeqFeatData::SubtypeValueToName(*it));
    }
    user.SetData().push_back(field);
}
 
 
void CAutoDefOptions::x_SetSuppressedFeatures(const CUser_field& field)
{
    ClearSuppressedFeatures();
 
    if (!field.IsSetData()) {
        return;
    }
    if (field.GetData().IsStr() && NStr::EqualNocase(field.GetData().GetStr(), "All")) {
        m_SuppressedFeatureSubtypes.push_back(CSeqFeatData::eSubtype_any);
        return;
    }
 
    if (!field.GetData().IsStrs()){
        return;
    }
 
    ITERATE(CUser_field::TData::TStrs, v, field.GetData().GetStrs()) {
        CSeqFeatData::ESubtype val = CSeqFeatData::SubtypeNameToValue(*v);
        if (val != CSeqFeatData::eSubtype_bad) {
            m_SuppressedFeatureSubtypes.push_back(val);
        }
    }
}
 
 
void CAutoDefOptions::AddSubSource(CSubSource::TSubtype subtype)
{
    m_SubSources.push_back(subtype);
}
 
 
void CAutoDefOptions::AddOrgMod(COrgMod::TSubtype subtype)
{
    m_OrgMods.push_back(subtype);
}
 
 
void CAutoDefOptions::ClearModifierList()
{
    m_OrgMods.clear();
    m_SubSources.clear();
}
 
 
const string kSubSources = "SubSources";
const string kOrgMods = "OrgMods";
 
void CAutoDefOptions::x_MakeModifierList(CUser_object& user) const
{
    try {
    CRef<CUser_field> field(new CUser_field());
    field->SetLabel().SetStr(GetFieldType(eOptionFieldType_ModifierList));
 
        if (!m_SubSources.empty()) {
            CRef<CUser_field> subsources(new CUser_field());
            subsources->SetLabel().SetStr(kSubSources);
            vector<string> vals;
            ITERATE(TSubSources, it, m_SubSources) {
                vals.push_back(CSubSource::GetSubtypeName(*it));
            }
            sort(vals.begin(), vals.end());
            vector<string>::iterator sort_it = std::unique(vals.begin(), vals.end());
            vals.resize(distance(vals.begin(), sort_it));
            ITERATE(vector<string>, it, vals) {
                subsources->SetData().SetStrs().push_back(*it);
            }
            field->SetData().SetFields().push_back(subsources);
        }
 
        if (!m_OrgMods.empty()) {
            CRef<CUser_field> orgmods(new CUser_field());
            orgmods->SetLabel().SetStr(kOrgMods);
            vector<string> vals;
            ITERATE(TOrgMods, it, m_OrgMods) {
                vals.push_back(COrgMod::GetSubtypeName(*it));
            }
            sort(vals.begin(), vals.end());
            vector<string>::iterator sort_it = std::unique(vals.begin(), vals.end());
            vals.resize(distance(vals.begin(), sort_it));
            ITERATE(vector<string>, it, vals) {
                orgmods->SetData().SetStrs().push_back(*it);
            }
            field->SetData().SetFields().push_back(orgmods);
        }
 
    if (field->IsSetData() && field->GetData().IsFields() && field->GetData().GetFields().size() > 0) {
        user.SetData().push_back(field);
    }
    } catch ( ... ) {
    }
}
 
 
void CAutoDefOptions::x_SetModifierList(const CUser_field& field)
{
    ClearModifierList();
 
    try {
    if (!field.IsSetData() || !field.GetData().IsFields()) {
        return;
    }
 
    ITERATE(CUser_field::TData::TFields, it, field.GetData().GetFields()) {
        if ((*it)->IsSetLabel() && (*it)->GetLabel().IsStr() &&
            (*it)->IsSetData() && (*it)->GetData().IsStrs()) {
            if (NStr::EqualNocase((*it)->GetLabel().GetStr(), kSubSources)) {
                ITERATE(CUser_field::TData::TStrs, s, (*it)->GetData().GetStrs()) {
                    CSubSource::TSubtype subtype = CSubSource::GetSubtypeValue(*s);
                    m_SubSources.push_back(subtype);
                }
            } else if (NStr::EqualNocase((*it)->GetLabel().GetStr(), kOrgMods)) {
                ITERATE(CUser_field::TData::TStrs, s, (*it)->GetData().GetStrs()) {
                    COrgMod::TSubtype subtype = COrgMod::GetSubtypeValue(*s);
                    m_OrgMods.push_back(subtype);
                }
            }
        }
    }
    } catch ( ... ) {
    }
}
 
 
CRef<CUser_field> CAutoDefOptions::x_MakeMaxMods() const
{
    CRef<CUser_field> field(new CUser_field());
    field->SetLabel().SetStr(GetFieldType(eOptionFieldType_MaxMods));
    field->SetData().SetInt(m_MaxMods);
    return field;
}
 
 
CRef<CUser_field> CAutoDefOptions::x_MakeTargetedLocusName() const
{
    CRef<CUser_field> field(new CUser_field());
    field->SetLabel().SetStr(GetFieldType(eOptionFieldType_TargetedLocusName));
    field->SetData().SetStr(m_TargetedLocusName);
    return field;
}
 
 
CRef<CUser_field> CAutoDefOptions::x_MakeCustomFeatureClause() const
{
    CRef<CUser_field> field(new CUser_field());
    field->SetLabel().SetStr(GetFieldType(eOptionFieldType_CustomFeatureClause));
    field->SetData().SetStr(m_CustomFeatureClause);
    return field;
}
 
 
 
END_SCOPE(objects)
END_NCBI_SCOPE